https://launchpad.net/ubuntu/+source/libgoby-java/3.3.1+dfsg2-11/+build/28446411
RUN: /usr/share/launchpad-buildd/bin/builder-prep 
Kernel version: Linux lcy02-amd64-047 5.4.0-182-generic #202-Ubuntu SMP Fri Apr 26 12:29:36 UTC 2024 x86_64
Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1.
Syncing the system clock with the buildd NTP service...
14 May 23:16:43 ntpdate[1911]: adjust time server 10.131.248.1 offset 0.004494 sec
RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28446411 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9
Creating target for build PACKAGEBUILD-28446411
RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28446411
Starting target for build PACKAGEBUILD-28446411
RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28446411 'deb http://ftpmaster.internal/ubuntu oracular main universe' 'deb http://ftpmaster.internal/ubuntu oracular-security main universe' 'deb http://ftpmaster.internal/ubuntu oracular-updates main universe' 'deb http://ftpmaster.internal/ubuntu oracular-proposed main universe'
Overriding sources.list in build-PACKAGEBUILD-28446411
RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28446411
Updating target for build PACKAGEBUILD-28446411
Get:1 http://ftpmaster.internal/ubuntu oracular InRelease [73.9 kB]
Get:2 http://ftpmaster.internal/ubuntu oracular-security InRelease [73.9 kB]
Get:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease [73.9 kB]
Get:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.9 kB]
Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 Packages [1395 kB]
Get:6 http://ftpmaster.internal/ubuntu oracular/main Translation-en [512 kB]
Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 Packages [15.2 MB]
Get:8 http://ftpmaster.internal/ubuntu oracular/universe Translation-en [6029 kB]
Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [224 kB]
Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main Translation-en [78.4 kB]
Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [1111 kB]
Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe Translation-en [412 kB]
Fetched 25.2 MB in 3s (7744 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
  libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
  libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30*
  libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3*
  libtirpc3* usrmerge*
The following NEW packages will be installed:
  cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++-13-x86-64-linux-gnu
  g++-x86-64-linux-gnu gcc-13-x86-64-linux-gnu gcc-14-base
  gcc-x86-64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64
  libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64
  libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64
  libtirpc3t64 libunistring5 perl-modules-5.38
The following packages will be upgraded:
  advancecomp apt apt-utils base-files base-passwd bash bash-completion
  binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils
  bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n
  debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-13
  gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init
  init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8
  libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils
  libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0
  libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12
  libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl
  libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgmp10
  libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgprofng0
  libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4
  libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0
  liblocale-gettext-perl liblockfile-bin liblockfile1 liblsan0 liblz4-1
  liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2
  libnss-nis libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin
  libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libquadmath0 libseccomp2
  libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1
  libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6
  libsystemd-shared libsystemd0 libtasn1-6 libtext-charwidth-perl
  libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1
  libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login
  logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl
  optipng passwd patch perl perl-base pinentry-curses procps psmisc
  readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev
  systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux
  uuid-runtime xz-utils zlib1g
177 upgraded, 23 newly installed, 14 to remove and 0 not upgraded.
Need to get 120 MB of archives.
After this operation, 61.0 MB of additional disk space will be used.
Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libtirpc-common all 1.3.4+ds-1.3 [8106 B]
Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3 [193 kB]
Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libnsl-dev amd64 1.3.0-3build3 [70.5 kB]
Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libnsl2 amd64 1.3.0-3build3 [41.4 kB]
Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.5 kB]
Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libgssapi-krb5-2 amd64 1.20.1-6ubuntu2 [142 kB]
Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libkrb5-3 amd64 1.20.1-6ubuntu2 [347 kB]
Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libk5crypto3 amd64 1.20.1-6ubuntu2 [81.7 kB]
Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libkrb5support0 amd64 1.20.1-6ubuntu2 [33.5 kB]
Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libargon2-1 amd64 0~20190702+dfsg-4build1 [20.8 kB]
Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libblkid1 amd64 2.39.3-9ubuntu6 [123 kB]
Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu2 [227 kB]
Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libselinux1 amd64 3.5-2ubuntu2 [79.6 kB]
Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libcap2 amd64 1:2.66-5ubuntu2 [30.0 kB]
Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libudev1 amd64 256~rc1-1~exp2ubuntu1 [188 kB]
Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-3ubuntu3 [139 kB]
Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libjson-c5 amd64 0.17-1build1 [35.3 kB]
Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 libuuid1 amd64 2.39.3-9ubuntu6 [35.2 kB]
Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 libcryptsetup12 amd64 2:2.7.0-1ubuntu4 [266 kB]
Get:20 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libacl1 amd64 2.3.2-2 [16.8 kB]
Get:21 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libapparmor1 amd64 4.0.1-0ubuntu1 [49.9 kB]
Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 libaudit-common all 1:3.1.2-2.1build1 [5736 B]
Get:23 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libcap-ng0 amd64 0.8.5-1 [15.2 kB]
Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 libaudit1 amd64 1:3.1.2-2.1build1 [46.9 kB]
Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 libcrypt-dev amd64 1:4.4.36-4build1 [112 kB]
Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 libcrypt1 amd64 1:4.4.36-4build1 [82.3 kB]
Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libmount1 amd64 2.39.3-9ubuntu6 [134 kB]
Get:28 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 perl-modules-5.38 all 5.38.2-4 [3110 kB]
Get:29 http://ftpmaster.internal/ubuntu oracular/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [734 kB]
Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libgdbm6t64 amd64 1.23-5.1build1 [34.4 kB]
Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libgdbm-compat4t64 amd64 1.23-5.1build1 [6710 B]
Get:32 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libperl5.38t64 amd64 5.38.2-4 [4870 kB]
Get:33 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 perl amd64 5.38.2-4 [231 kB]
Get:34 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 perl-base amd64 5.38.2-4 [1823 kB]
Get:35 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 liblocale-gettext-perl amd64 1.07-7 [15.6 kB]
Get:36 http://ftpmaster.internal/ubuntu oracular/main amd64 libtext-iconv-perl amd64 1.7-8build3 [13.5 kB]
Get:37 http://ftpmaster.internal/ubuntu oracular/main amd64 libtext-charwidth-perl amd64 0.04-11build3 [9358 B]
Get:38 http://ftpmaster.internal/ubuntu oracular/universe amd64 libnss-nisplus amd64 1.3-5build1 [22.4 kB]
Get:39 http://ftpmaster.internal/ubuntu oracular/universe amd64 libnss-nis amd64 3.1-0ubuntu7 [26.5 kB]
Get:40 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-0ubuntu8.1 [20.4 kB]
Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu7 [67.4 kB]
Get:42 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-0ubuntu8.1 [2124 kB]
Get:43 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-0ubuntu8.1 [3265 kB]
Get:44 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-0ubuntu8.1 [682 kB]
Get:45 http://ftpmaster.internal/ubuntu oracular/main amd64 openssl amd64 3.0.13-0ubuntu3 [1002 kB]
Get:46 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libsystemd-shared amd64 256~rc1-1~exp2ubuntu1 [2183 kB]
Get:47 http://ftpmaster.internal/ubuntu oracular/main amd64 liblzma5 amd64 5.6.1+really5.4.5-1 [127 kB]
Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 libkmod2 amd64 31+20240202-2ubuntu7 [51.7 kB]
Get:49 http://ftpmaster.internal/ubuntu oracular/main amd64 libssl3t64 amd64 3.0.13-0ubuntu3 [1936 kB]
Get:50 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 systemd-dev all 256~rc1-1~exp2ubuntu1 [105 kB]
Get:51 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 systemd-sysv amd64 256~rc1-1~exp2ubuntu1 [11.9 kB]
Get:52 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 systemd amd64 256~rc1-1~exp2ubuntu1 [3641 kB]
Get:53 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libsystemd0 amd64 256~rc1-1~exp2ubuntu1 [439 kB]
Get:54 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libapt-pkg6.0t64 amd64 2.9.3 [1014 kB]
Get:55 http://ftpmaster.internal/ubuntu oracular/main amd64 libnettle8t64 amd64 3.9.1-2.2build1 [182 kB]
Get:56 http://ftpmaster.internal/ubuntu oracular/main amd64 libhogweed6t64 amd64 3.9.1-2.2build1 [199 kB]
Get:57 http://ftpmaster.internal/ubuntu oracular/main amd64 libp11-kit0 amd64 0.25.3-4ubuntu2 [299 kB]
Get:58 http://ftpmaster.internal/ubuntu oracular/main amd64 libunistring5 amd64 1.2-1 [539 kB]
Get:59 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgnutls30t64 amd64 3.8.5-2ubuntu1 [1009 kB]
Get:60 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 apt amd64 2.9.3 [1403 kB]
Get:61 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 apt-utils amd64 2.9.3 [223 kB]
Get:62 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-modules-bin amd64 1.5.3-7ubuntu1 [51.9 kB]
Get:63 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-modules amd64 1.5.3-7ubuntu1 [284 kB]
Get:64 http://ftpmaster.internal/ubuntu oracular/main amd64 bzip2 amd64 1.0.8-5.1 [34.5 kB]
Get:65 http://ftpmaster.internal/ubuntu oracular/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [34.3 kB]
Get:66 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 gcc-14-base amd64 14-20240429-1ubuntu1 [48.0 kB]
Get:67 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgcc-s1 amd64 14-20240429-1ubuntu1 [78.3 kB]
Get:68 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgpg-error-l10n all 1.49-2 [8228 B]
Get:69 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgpg-error0 amd64 1.49-2 [70.9 kB]
Get:70 http://ftpmaster.internal/ubuntu oracular/main amd64 libgcrypt20 amd64 1.10.3-2build1 [532 kB]
Get:71 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 liblz4-1 amd64 1.9.4-2 [62.9 kB]
Get:72 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libstdc++6 amd64 14-20240429-1ubuntu1 [794 kB]
Get:73 http://ftpmaster.internal/ubuntu oracular/main amd64 libxxhash0 amd64 0.8.2-2build1 [24.1 kB]
Get:74 http://ftpmaster.internal/ubuntu oracular/main amd64 libzstd1 amd64 1.5.5+dfsg2-2build1 [299 kB]
Get:75 http://ftpmaster.internal/ubuntu oracular/main amd64 zlib1g amd64 1:1.3.dfsg-3.1ubuntu2 [62.8 kB]
Get:76 http://ftpmaster.internal/ubuntu oracular/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2ubuntu6 [253 kB]
Get:77 http://ftpmaster.internal/ubuntu oracular/main amd64 libffi8 amd64 3.4.6-1build1 [24.7 kB]
Get:78 http://ftpmaster.internal/ubuntu oracular/main amd64 libidn2-0 amd64 2.3.7-2build1 [66.2 kB]
Get:79 http://ftpmaster.internal/ubuntu oracular/main amd64 libtasn1-6 amd64 4.19.0-3build1 [43.9 kB]
Get:80 http://ftpmaster.internal/ubuntu oracular/main amd64 libdebconfclient0 amd64 0.271ubuntu3 [11.4 kB]
Get:81 http://ftpmaster.internal/ubuntu oracular/main amd64 base-passwd amd64 3.6.3build1 [51.1 kB]
Get:82 http://ftpmaster.internal/ubuntu oracular/main amd64 libassuan0 amd64 2.5.6-1build1 [37.3 kB]
Get:83 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libsqlite3-0 amd64 3.45.3-1 [701 kB]
Get:84 http://ftpmaster.internal/ubuntu oracular/main amd64 gpg amd64 2.4.4-2ubuntu17 [565 kB]
Get:85 http://ftpmaster.internal/ubuntu oracular/main amd64 libreadline8t64 amd64 8.2-4build1 [153 kB]
Get:86 http://ftpmaster.internal/ubuntu oracular/main amd64 readline-common all 8.2-4build1 [56.5 kB]
Get:87 http://ftpmaster.internal/ubuntu oracular/main amd64 libncursesw6 amd64 6.4+20240113-1ubuntu2 [148 kB]
Get:88 http://ftpmaster.internal/ubuntu oracular/main amd64 libtinfo6 amd64 6.4+20240113-1ubuntu2 [108 kB]
Get:89 http://ftpmaster.internal/ubuntu oracular/main amd64 gpg-agent amd64 2.4.4-2ubuntu17 [227 kB]
Get:90 http://ftpmaster.internal/ubuntu oracular/main amd64 gpgconf amd64 2.4.4-2ubuntu17 [103 kB]
Get:91 http://ftpmaster.internal/ubuntu oracular/main amd64 pinentry-curses amd64 1.2.1-3ubuntu5 [35.2 kB]
Get:92 http://ftpmaster.internal/ubuntu oracular/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB]
Get:93 http://ftpmaster.internal/ubuntu oracular/main amd64 libnpth0t64 amd64 1.6-3.1build1 [8378 B]
Get:94 http://ftpmaster.internal/ubuntu oracular/main amd64 gpgv amd64 2.4.4-2ubuntu17 [157 kB]
Get:95 http://ftpmaster.internal/ubuntu oracular/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB]
Get:96 http://ftpmaster.internal/ubuntu oracular/main amd64 libseccomp2 amd64 2.5.5-1ubuntu3 [50.3 kB]
Get:97 http://ftpmaster.internal/ubuntu oracular/main amd64 debconf-i18n all 1.5.86ubuntu1 [205 kB]
Get:98 http://ftpmaster.internal/ubuntu oracular/main amd64 debconf all 1.5.86ubuntu1 [124 kB]
Get:99 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam0g amd64 1.5.3-7ubuntu1 [67.8 kB]
Get:100 http://ftpmaster.internal/ubuntu oracular/main amd64 libfdisk1 amd64 2.39.3-9ubuntu6 [146 kB]
Get:101 http://ftpmaster.internal/ubuntu oracular/main amd64 mount amd64 2.39.3-9ubuntu6 [118 kB]
Get:102 http://ftpmaster.internal/ubuntu oracular/main amd64 libcom-err2 amd64 1.47.0-2.4~exp1ubuntu4 [22.8 kB]
Get:103 http://ftpmaster.internal/ubuntu oracular/main amd64 libkeyutils1 amd64 1.6.3-3build1 [9490 B]
Get:104 http://ftpmaster.internal/ubuntu oracular/main amd64 linux-libc-dev amd64 6.8.0-31.31 [1598 kB]
Get:105 http://ftpmaster.internal/ubuntu oracular/main amd64 base-files amd64 13.1ubuntu1 [73.8 kB]
Get:106 http://ftpmaster.internal/ubuntu oracular/main amd64 debianutils amd64 5.17build1 [89.9 kB]
Get:107 http://ftpmaster.internal/ubuntu oracular/main amd64 bash amd64 5.2.21-2ubuntu4 [794 kB]
Get:108 http://ftpmaster.internal/ubuntu oracular/main amd64 bsdutils amd64 1:2.39.3-9ubuntu6 [95.0 kB]
Get:109 http://ftpmaster.internal/ubuntu oracular/main amd64 coreutils amd64 9.4-3ubuntu6 [1412 kB]
Get:110 http://ftpmaster.internal/ubuntu oracular/main amd64 tar amd64 1.35+dfsg-3build1 [253 kB]
Get:111 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 dpkg amd64 1.22.6ubuntu10 [1283 kB]
Get:112 http://ftpmaster.internal/ubuntu oracular/main amd64 dash amd64 0.5.12-6ubuntu5 [89.8 kB]
Get:113 http://ftpmaster.internal/ubuntu oracular/main amd64 diffutils amd64 1:3.10-1build1 [177 kB]
Get:114 http://ftpmaster.internal/ubuntu oracular/main amd64 findutils amd64 4.9.0-5build1 [298 kB]
Get:115 http://ftpmaster.internal/ubuntu oracular/main amd64 grep amd64 3.11-4build1 [162 kB]
Get:116 http://ftpmaster.internal/ubuntu oracular/main amd64 gzip amd64 1.12-1ubuntu3 [98.8 kB]
Get:117 http://ftpmaster.internal/ubuntu oracular/main amd64 hostname amd64 3.23+nmu2ubuntu2 [11.1 kB]
Get:118 http://ftpmaster.internal/ubuntu oracular/main amd64 login amd64 1:4.13+dfsg1-4ubuntu3 [202 kB]
Get:119 http://ftpmaster.internal/ubuntu oracular/main amd64 ncurses-bin amd64 6.4+20240113-1ubuntu2 [188 kB]
Get:120 http://ftpmaster.internal/ubuntu oracular/main amd64 sed amd64 4.9-2build1 [193 kB]
Get:121 http://ftpmaster.internal/ubuntu oracular/main amd64 util-linux amd64 2.39.3-9ubuntu6 [1127 kB]
Get:122 http://ftpmaster.internal/ubuntu oracular/main amd64 ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB]
Get:123 http://ftpmaster.internal/ubuntu oracular/main amd64 sysvinit-utils amd64 3.08-6ubuntu3 [34.2 kB]
Get:124 http://ftpmaster.internal/ubuntu oracular/main amd64 logsave amd64 1.47.0-2.4~exp1ubuntu4 [22.5 kB]
Get:125 http://ftpmaster.internal/ubuntu oracular/main amd64 libext2fs2t64 amd64 1.47.0-2.4~exp1ubuntu4 [222 kB]
Get:126 http://ftpmaster.internal/ubuntu oracular/main amd64 e2fsprogs amd64 1.47.0-2.4~exp1ubuntu4 [601 kB]
Get:127 http://ftpmaster.internal/ubuntu oracular/main amd64 optipng amd64 0.7.8+ds-1build2 [110 kB]
Get:128 http://ftpmaster.internal/ubuntu oracular/main amd64 libpng16-16t64 amd64 1.6.43-5build1 [187 kB]
Get:129 http://ftpmaster.internal/ubuntu oracular/main amd64 init amd64 1.66ubuntu1 [6186 B]
Get:130 http://ftpmaster.internal/ubuntu oracular/main amd64 libsmartcols1 amd64 2.39.3-9ubuntu6 [64.8 kB]
Get:131 http://ftpmaster.internal/ubuntu oracular/main amd64 uuid-runtime amd64 2.39.3-9ubuntu6 [33.1 kB]
Get:132 http://ftpmaster.internal/ubuntu oracular/main amd64 libattr1 amd64 1:2.5.2-1build1 [11.3 kB]
Get:133 http://ftpmaster.internal/ubuntu oracular/main amd64 libmd0 amd64 1.1.0-2build1 [27.0 kB]
Get:134 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-runtime all 1.5.3-7ubuntu1 [40.8 kB]
Get:135 http://ftpmaster.internal/ubuntu oracular/main amd64 libsemanage-common all 3.5-1build5 [10.1 kB]
Get:136 http://ftpmaster.internal/ubuntu oracular/main amd64 libsepol2 amd64 3.5-2build1 [303 kB]
Get:137 http://ftpmaster.internal/ubuntu oracular/main amd64 libsemanage2 amd64 3.5-1build5 [93.2 kB]
Get:138 http://ftpmaster.internal/ubuntu oracular/main amd64 passwd amd64 1:4.13+dfsg1-4ubuntu3 [845 kB]
Get:139 http://ftpmaster.internal/ubuntu oracular/main amd64 libproc2-0 amd64 2:4.0.4-4ubuntu3 [59.1 kB]
Get:140 http://ftpmaster.internal/ubuntu oracular/main amd64 libss2 amd64 1.47.0-2.4~exp1ubuntu4 [17.0 kB]
Get:141 http://ftpmaster.internal/ubuntu oracular/main amd64 mawk amd64 1.3.4.20240123-1build1 [127 kB]
Get:142 http://ftpmaster.internal/ubuntu oracular/main amd64 procps amd64 2:4.0.4-4ubuntu3 [708 kB]
Get:143 http://ftpmaster.internal/ubuntu oracular/main amd64 sensible-utils all 0.0.22 [22.5 kB]
Get:144 http://ftpmaster.internal/ubuntu oracular/main amd64 ca-certificates all 20240203 [159 kB]
Get:145 http://ftpmaster.internal/ubuntu oracular/main amd64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB]
Get:146 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 tzdata all 2024a-4ubuntu1 [274 kB]
Get:147 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 bash-completion all 1:2.13.0-1 [205 kB]
Get:148 http://ftpmaster.internal/ubuntu oracular/main amd64 bsdextrautils amd64 2.39.3-9ubuntu6 [73.8 kB]
Get:149 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpm2 amd64 1.20.7-11 [14.1 kB]
Get:150 http://ftpmaster.internal/ubuntu oracular/main amd64 libip4tc2 amd64 1.8.10-3ubuntu2 [23.3 kB]
Get:151 http://ftpmaster.internal/ubuntu oracular/main amd64 libjansson4 amd64 2.14-2build2 [32.8 kB]
Get:152 http://ftpmaster.internal/ubuntu oracular/main amd64 psmisc amd64 23.7-1build1 [179 kB]
Get:153 http://ftpmaster.internal/ubuntu oracular/main amd64 xz-utils amd64 5.6.1+really5.4.5-1 [267 kB]
Get:154 http://ftpmaster.internal/ubuntu oracular/main amd64 advancecomp amd64 2.5-1build1 [182 kB]
Get:155 http://ftpmaster.internal/ubuntu oracular/main amd64 libgprofng0 amd64 2.42-4ubuntu2 [851 kB]
Get:156 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf0 amd64 2.42-4ubuntu2 [94.5 kB]
Get:157 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf-nobfd0 amd64 2.42-4ubuntu2 [97.1 kB]
Get:158 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-x86-64-linux-gnu amd64 2.42-4ubuntu2 [2469 kB]
Get:159 http://ftpmaster.internal/ubuntu oracular/main amd64 libbinutils amd64 2.42-4ubuntu2 [572 kB]
Get:160 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils amd64 2.42-4ubuntu2 [18.0 kB]
Get:161 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-common amd64 2.42-4ubuntu2 [239 kB]
Get:162 http://ftpmaster.internal/ubuntu oracular/main amd64 libsframe1 amd64 2.42-4ubuntu2 [14.8 kB]
Get:163 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libubsan1 amd64 14-20240429-1ubuntu1 [1175 kB]
Get:164 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 g++-13 amd64 13.2.0-25ubuntu1 [15.6 kB]
Get:165 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libstdc++-13-dev amd64 13.2.0-25ubuntu1 [2423 kB]
Get:166 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgomp1 amd64 14-20240429-1ubuntu1 [148 kB]
Get:167 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libitm1 amd64 14-20240429-1ubuntu1 [28.9 kB]
Get:168 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libatomic1 amd64 14-20240429-1ubuntu1 [10.4 kB]
Get:169 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libasan8 amd64 14-20240429-1ubuntu1 [3025 kB]
Get:170 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 liblsan0 amd64 14-20240429-1ubuntu1 [1313 kB]
Get:171 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libhwasan0 amd64 14-20240429-1ubuntu1 [1632 kB]
Get:172 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libquadmath0 amd64 14-20240429-1ubuntu1 [153 kB]
Get:173 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 gcc-13 amd64 13.2.0-25ubuntu1 [488 kB]
Get:174 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgcc-13-dev amd64 13.2.0-25ubuntu1 [2688 kB]
Get:175 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libtsan2 amd64 14-20240429-1ubuntu1 [2735 kB]
Get:176 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libcc1-0 amd64 14-20240429-1ubuntu1 [47.7 kB]
Get:177 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 cpp-13 amd64 13.2.0-25ubuntu1 [1032 B]
Get:178 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 gcc-13-base amd64 13.2.0-25ubuntu1 [49.9 kB]
Get:179 http://ftpmaster.internal/ubuntu oracular/main amd64 libisl23 amd64 0.26-3build1 [680 kB]
Get:180 http://ftpmaster.internal/ubuntu oracular/main amd64 libmpfr6 amd64 4.2.1-1build1 [355 kB]
Get:181 http://ftpmaster.internal/ubuntu oracular/main amd64 libmpc3 amd64 1.3.1-1build1 [54.5 kB]
Get:182 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-25ubuntu1 [21.1 MB]
Get:183 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-25ubuntu1 [12.2 MB]
Get:184 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-25ubuntu1 [10.7 MB]
Get:185 http://ftpmaster.internal/ubuntu oracular/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B]
Get:186 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B]
Get:187 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB]
Get:188 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B]
Get:189 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B]
Get:190 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B]
Get:191 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 dpkg-dev all 1.22.6ubuntu10 [1074 kB]
Get:192 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libdpkg-perl all 1.22.6ubuntu10 [269 kB]
Get:193 http://ftpmaster.internal/ubuntu oracular/main amd64 patch amd64 2.7.6-7build3 [104 kB]
Get:194 http://ftpmaster.internal/ubuntu oracular/main amd64 make amd64 4.3-4.1build2 [180 kB]
Get:195 http://ftpmaster.internal/ubuntu oracular/main amd64 lto-disabled-list all 48 [12.3 kB]
Get:196 http://ftpmaster.internal/ubuntu oracular/main amd64 libfakeroot amd64 1.34-1 [32.4 kB]
Get:197 http://ftpmaster.internal/ubuntu oracular/main amd64 fakeroot amd64 1.34-1 [67.2 kB]
Get:198 http://ftpmaster.internal/ubuntu oracular/main amd64 liblockfile-bin amd64 1.17-1build3 [11.2 kB]
Get:199 http://ftpmaster.internal/ubuntu oracular/main amd64 liblockfile1 amd64 1.17-1build3 [6840 B]
Get:200 http://ftpmaster.internal/ubuntu oracular/main amd64 lockfile-progs amd64 0.1.19+nmu1 [8854 B]
Preconfiguring packages ...
Fetched 120 MB in 6s (21.3 MB/s)
(Reading database ... 13648 files and directories currently installed.)
Preparing to unpack .../libtirpc-common_1.3.4+ds-1.3_all.deb ...
Unpacking libtirpc-common (1.3.4+ds-1.3) over (1.3.3+ds-1) ...
Preparing to unpack .../libtirpc-dev_1.3.4+ds-1.3_amd64.deb ...
Unpacking libtirpc-dev:amd64 (1.3.4+ds-1.3) over (1.3.3+ds-1) ...
Preparing to unpack .../libnsl-dev_1.3.0-3build3_amd64.deb ...
Unpacking libnsl-dev:amd64 (1.3.0-3build3) over (1.3.0-2build2) ...
Preparing to unpack .../libnsl2_1.3.0-3build3_amd64.deb ...
Unpacking libnsl2:amd64 (1.3.0-3build3) over (1.3.0-2build2) ...
dpkg: libtirpc3:amd64: dependency problems, but removing anyway as you requested:
 libnss-nisplus:amd64 depends on libtirpc3 (>= 1.0.2).

(Reading database ... 13648 files and directories currently installed.)
Removing libtirpc3:amd64 (1.3.3+ds-1) ...
Selecting previously unselected package libtirpc3t64:amd64.
(Reading database ... 13642 files and directories currently installed.)
Preparing to unpack .../0-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ...
Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ...
Preparing to unpack .../1-libgssapi-krb5-2_1.20.1-6ubuntu2_amd64.deb ...
Unpacking libgssapi-krb5-2:amd64 (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ...
Preparing to unpack .../2-libkrb5-3_1.20.1-6ubuntu2_amd64.deb ...
Unpacking libkrb5-3:amd64 (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ...
Preparing to unpack .../3-libk5crypto3_1.20.1-6ubuntu2_amd64.deb ...
Unpacking libk5crypto3:amd64 (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ...
Preparing to unpack .../4-libkrb5support0_1.20.1-6ubuntu2_amd64.deb ...
Unpacking libkrb5support0:amd64 (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ...
Preparing to unpack .../5-libargon2-1_0~20190702+dfsg-4build1_amd64.deb ...
Unpacking libargon2-1:amd64 (0~20190702+dfsg-4build1) over (0~20190702+dfsg-3) ...
Preparing to unpack .../6-libblkid1_2.39.3-9ubuntu6_amd64.deb ...
Unpacking libblkid1:amd64 (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ...
Setting up libblkid1:amd64 (2.39.3-9ubuntu6) ...
(Reading database ... 13653 files and directories currently installed.)
Preparing to unpack .../libpcre2-8-0_10.42-4ubuntu2_amd64.deb ...
Unpacking libpcre2-8-0:amd64 (10.42-4ubuntu2) over (10.42-4) ...
Setting up libpcre2-8-0:amd64 (10.42-4ubuntu2) ...
(Reading database ... 13653 files and directories currently installed.)
Preparing to unpack .../libselinux1_3.5-2ubuntu2_amd64.deb ...
Unpacking libselinux1:amd64 (3.5-2ubuntu2) over (3.5-1) ...
Setting up libselinux1:amd64 (3.5-2ubuntu2) ...
(Reading database ... 13654 files and directories currently installed.)
Preparing to unpack .../libcap2_1%3a2.66-5ubuntu2_amd64.deb ...
Unpacking libcap2:amd64 (1:2.66-5ubuntu2) over (1:2.66-4ubuntu1) ...
Setting up libcap2:amd64 (1:2.66-5ubuntu2) ...
(Reading database ... 13654 files and directories currently installed.)
Preparing to unpack .../libudev1_256~rc1-1~exp2ubuntu1_amd64.deb ...
Unpacking libudev1:amd64 (256~rc1-1~exp2ubuntu1) over (253.5-1ubuntu6) ...
Setting up libudev1:amd64 (256~rc1-1~exp2ubuntu1) ...
(Reading database ... 13654 files and directories currently installed.)
Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-3ubuntu3_amd64.deb ...
Unpacking libdevmapper1.02.1:amd64 (2:1.02.185-3ubuntu3) over (2:1.02.185-2ubuntu1) ...
Preparing to unpack .../libjson-c5_0.17-1build1_amd64.deb ...
Unpacking libjson-c5:amd64 (0.17-1build1) over (0.17-1) ...
Preparing to unpack .../libuuid1_2.39.3-9ubuntu6_amd64.deb ...
Unpacking libuuid1:amd64 (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ...
Setting up libuuid1:amd64 (2.39.3-9ubuntu6) ...
(Reading database ... 13654 files and directories currently installed.)
Preparing to unpack .../libcryptsetup12_2%3a2.7.0-1ubuntu4_amd64.deb ...
Unpacking libcryptsetup12:amd64 (2:2.7.0-1ubuntu4) over (2:2.6.1-4ubuntu3) ...
Preparing to unpack .../libacl1_2.3.2-2_amd64.deb ...
Unpacking libacl1:amd64 (2.3.2-2) over (2.3.1-3) ...
Setting up libacl1:amd64 (2.3.2-2) ...
(Reading database ... 13654 files and directories currently installed.)
Preparing to unpack .../libapparmor1_4.0.1-0ubuntu1_amd64.deb ...
Unpacking libapparmor1:amd64 (4.0.1-0ubuntu1) over (4.0.0~alpha2-0ubuntu5) ...
Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1build1_all.deb ...
Unpacking libaudit-common (1:3.1.2-2.1build1) over (1:3.1.1-1) ...
Setting up libaudit-common (1:3.1.2-2.1build1) ...
(Reading database ... 13654 files and directories currently installed.)
Preparing to unpack .../libcap-ng0_0.8.5-1_amd64.deb ...
Unpacking libcap-ng0:amd64 (0.8.5-1) over (0.8.3-1build2) ...
Setting up libcap-ng0:amd64 (0.8.5-1) ...
(Reading database ... 13654 files and directories currently installed.)
Preparing to unpack .../libaudit1_1%3a3.1.2-2.1build1_amd64.deb ...
Unpacking libaudit1:amd64 (1:3.1.2-2.1build1) over (1:3.1.1-1) ...
Setting up libaudit1:amd64 (1:3.1.2-2.1build1) ...
(Reading database ... 13654 files and directories currently installed.)
Preparing to unpack .../libcrypt-dev_1%3a4.4.36-4build1_amd64.deb ...
Unpacking libcrypt-dev:amd64 (1:4.4.36-4build1) over (1:4.4.36-2) ...
Preparing to unpack .../libcrypt1_1%3a4.4.36-4build1_amd64.deb ...
Unpacking libcrypt1:amd64 (1:4.4.36-4build1) over (1:4.4.36-2) ...
Setting up libcrypt1:amd64 (1:4.4.36-4build1) ...
(Reading database ... 13654 files and directories currently installed.)
Preparing to unpack .../libmount1_2.39.3-9ubuntu6_amd64.deb ...
Unpacking libmount1:amd64 (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ...
Setting up libmount1:amd64 (2.39.3-9ubuntu6) ...
(Reading database ... 13654 files and directories currently installed.)
Preparing to unpack .../perl_5.38.2-4_amd64.deb ...
Unpacking perl (5.38.2-4) over (5.36.0-9ubuntu1) ...
Selecting previously unselected package perl-modules-5.38.
Preparing to unpack .../perl-modules-5.38_5.38.2-4_all.deb ...
Unpacking perl-modules-5.38 (5.38.2-4) ...
dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested:
 libperl5.36:amd64 depends on libdb5.3.
 libpam-modules:amd64 depends on libdb5.3.
 apt-utils depends on libdb5.3.

(Reading database ... 15066 files and directories currently installed.)
Removing libdb5.3:amd64 (5.3.28+dfsg2-2) ...
Selecting previously unselected package libdb5.3t64:amd64.
(Reading database ... 15060 files and directories currently installed.)
Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_amd64.deb ...
Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-7) ...
Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-7) ...
dpkg: libgdbm6:amd64: dependency problems, but removing anyway as you requested:
 libperl5.36:amd64 depends on libgdbm6 (>= 1.21).
 libgdbm-compat4:amd64 depends on libgdbm6 (>= 1.16).

(Reading database ... 15066 files and directories currently installed.)
Removing libgdbm6:amd64 (1.23-3) ...
Selecting previously unselected package libgdbm6t64:amd64.
(Reading database ... 15061 files and directories currently installed.)
Preparing to unpack .../libgdbm6t64_1.23-5.1build1_amd64.deb ...
Unpacking libgdbm6t64:amd64 (1.23-5.1build1) ...
dpkg: libgdbm-compat4:amd64: dependency problems, but removing anyway as you requested:
 libperl5.36:amd64 depends on libgdbm-compat4 (>= 1.18-3).

(Reading database ... 15067 files and directories currently installed.)
Removing libgdbm-compat4:amd64 (1.23-3) ...
Selecting previously unselected package libgdbm-compat4t64:amd64.
(Reading database ... 15062 files and directories currently installed.)
Preparing to unpack .../libgdbm-compat4t64_1.23-5.1build1_amd64.deb ...
Unpacking libgdbm-compat4t64:amd64 (1.23-5.1build1) ...
Selecting previously unselected package libperl5.38t64:amd64.
Preparing to unpack .../libperl5.38t64_5.38.2-4_amd64.deb ...
Unpacking libperl5.38t64:amd64 (5.38.2-4) ...
Preparing to unpack .../perl-base_5.38.2-4_amd64.deb ...
Unpacking perl-base (5.38.2-4) over (5.36.0-9ubuntu1) ...
Setting up perl-base (5.38.2-4) ...
(Reading database ... 15593 files and directories currently installed.)
Preparing to unpack .../0-liblocale-gettext-perl_1.07-7_amd64.deb ...
Unpacking liblocale-gettext-perl (1.07-7) over (1.07-6) ...
Preparing to unpack .../1-libtext-iconv-perl_1.7-8build3_amd64.deb ...
Unpacking libtext-iconv-perl:amd64 (1.7-8build3) over (1.7-8) ...
Preparing to unpack .../2-libtext-charwidth-perl_0.04-11build3_amd64.deb ...
Unpacking libtext-charwidth-perl:amd64 (0.04-11build3) over (0.04-11) ...
Preparing to unpack .../3-libnss-nisplus_1.3-5build1_amd64.deb ...
Unpacking libnss-nisplus:amd64 (1.3-5build1) over (1.3-0ubuntu6) ...
Preparing to unpack .../4-libnss-nis_3.1-0ubuntu7_amd64.deb ...
Unpacking libnss-nis:amd64 (3.1-0ubuntu7) over (3.1-0ubuntu6) ...
Preparing to unpack .../5-libc-dev-bin_2.39-0ubuntu8.1_amd64.deb ...
Unpacking libc-dev-bin (2.39-0ubuntu8.1) over (2.38-1ubuntu6) ...
Preparing to unpack .../6-rpcsvc-proto_1.4.2-0ubuntu7_amd64.deb ...
Unpacking rpcsvc-proto (1.4.2-0ubuntu7) over (1.4.2-0ubuntu6) ...
Preparing to unpack .../7-libc6-dev_2.39-0ubuntu8.1_amd64.deb ...
Unpacking libc6-dev:amd64 (2.39-0ubuntu8.1) over (2.38-1ubuntu6) ...
Preparing to unpack .../8-libc6_2.39-0ubuntu8.1_amd64.deb ...
Unpacking libc6:amd64 (2.39-0ubuntu8.1) over (2.38-1ubuntu6) ...
Setting up libc6:amd64 (2.39-0ubuntu8.1) ...
(Reading database ... 15601 files and directories currently installed.)
Preparing to unpack .../libc-bin_2.39-0ubuntu8.1_amd64.deb ...
Unpacking libc-bin (2.39-0ubuntu8.1) over (2.38-1ubuntu6) ...
Setting up libc-bin (2.39-0ubuntu8.1) ...
(Reading database ... 15601 files and directories currently installed.)
Preparing to unpack .../openssl_3.0.13-0ubuntu3_amd64.deb ...
Unpacking openssl (3.0.13-0ubuntu3) over (3.0.10-1ubuntu2) ...
Preparing to unpack .../libsystemd-shared_256~rc1-1~exp2ubuntu1_amd64.deb ...
Unpacking libsystemd-shared:amd64 (256~rc1-1~exp2ubuntu1) over (253.5-1ubuntu6) ...
Preparing to unpack .../liblzma5_5.6.1+really5.4.5-1_amd64.deb ...
Unpacking liblzma5:amd64 (5.6.1+really5.4.5-1) over (5.4.1-0.2) ...
Setting up liblzma5:amd64 (5.6.1+really5.4.5-1) ...
(Reading database ... 15600 files and directories currently installed.)
Preparing to unpack .../libkmod2_31+20240202-2ubuntu7_amd64.deb ...
Unpacking libkmod2:amd64 (31+20240202-2ubuntu7) over (30+20230519-1ubuntu3) ...
dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested:
 systemd depends on libssl3 (>= 3.0.0).

(Reading database ... 15600 files and directories currently installed.)
Removing libssl3:amd64 (3.0.10-1ubuntu2) ...
Selecting previously unselected package libssl3t64:amd64.
(Reading database ... 15589 files and directories currently installed.)
Preparing to unpack .../libssl3t64_3.0.13-0ubuntu3_amd64.deb ...
Unpacking libssl3t64:amd64 (3.0.13-0ubuntu3) ...
Setting up libssl3t64:amd64 (3.0.13-0ubuntu3) ...
(Reading database ... 15602 files and directories currently installed.)
Preparing to unpack .../systemd-dev_256~rc1-1~exp2ubuntu1_all.deb ...
Unpacking systemd-dev (256~rc1-1~exp2ubuntu1) over (253.5-1ubuntu6) ...
Preparing to unpack .../systemd-sysv_256~rc1-1~exp2ubuntu1_amd64.deb ...
Unpacking systemd-sysv (256~rc1-1~exp2ubuntu1) over (253.5-1ubuntu6) ...
Preparing to unpack .../systemd_256~rc1-1~exp2ubuntu1_amd64.deb ...
Unpacking systemd (256~rc1-1~exp2ubuntu1) over (253.5-1ubuntu6) ...
dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/sockets.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/multi-user.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/journald.conf.d': Directory not empty
dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty
Preparing to unpack .../libsystemd0_256~rc1-1~exp2ubuntu1_amd64.deb ...
Unpacking libsystemd0:amd64 (256~rc1-1~exp2ubuntu1) over (253.5-1ubuntu6) ...
Setting up libsystemd0:amd64 (256~rc1-1~exp2ubuntu1) ...
dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested:
 apt depends on libgnutls30 (>= 3.7.5).

(Reading database ... 15810 files and directories currently installed.)
Removing libgnutls30:amd64 (3.8.1-4ubuntu1) ...
Removing libhogweed6:amd64 (3.9.1-2) ...
Removing libnettle8:amd64 (3.9.1-2) ...
dpkg: libapt-pkg6.0:amd64: dependency problems, but removing anyway as you requested:
 apt-utils depends on libapt-pkg6.0 (>= 2.7.3).
 apt depends on libapt-pkg6.0 (>= 2.7.3).

Removing libapt-pkg6.0:amd64 (2.7.3) ...
Selecting previously unselected package libapt-pkg6.0t64:amd64.
(Reading database ... 15739 files and directories currently installed.)
Preparing to unpack .../libapt-pkg6.0t64_2.9.3_amd64.deb ...
Unpacking libapt-pkg6.0t64:amd64 (2.9.3) ...
Setting up libapt-pkg6.0t64:amd64 (2.9.3) ...
Selecting previously unselected package libnettle8t64:amd64.
(Reading database ... 15789 files and directories currently installed.)
Preparing to unpack .../libnettle8t64_3.9.1-2.2build1_amd64.deb ...
Unpacking libnettle8t64:amd64 (3.9.1-2.2build1) ...
Setting up libnettle8t64:amd64 (3.9.1-2.2build1) ...
Selecting previously unselected package libhogweed6t64:amd64.
(Reading database ... 15797 files and directories currently installed.)
Preparing to unpack .../libhogweed6t64_3.9.1-2.2build1_amd64.deb ...
Unpacking libhogweed6t64:amd64 (3.9.1-2.2build1) ...
Setting up libhogweed6t64:amd64 (3.9.1-2.2build1) ...
(Reading database ... 15803 files and directories currently installed.)
Preparing to unpack .../libp11-kit0_0.25.3-4ubuntu2_amd64.deb ...
Unpacking libp11-kit0:amd64 (0.25.3-4ubuntu2) over (0.25.0-4ubuntu1) ...
Setting up libp11-kit0:amd64 (0.25.3-4ubuntu2) ...
Selecting previously unselected package libunistring5:amd64.
(Reading database ... 15803 files and directories currently installed.)
Preparing to unpack .../libunistring5_1.2-1_amd64.deb ...
Unpacking libunistring5:amd64 (1.2-1) ...
Setting up libunistring5:amd64 (1.2-1) ...
Selecting previously unselected package libgnutls30t64:amd64.
(Reading database ... 15808 files and directories currently installed.)
Preparing to unpack .../libgnutls30t64_3.8.5-2ubuntu1_amd64.deb ...
Unpacking libgnutls30t64:amd64 (3.8.5-2ubuntu1) ...
Setting up libgnutls30t64:amd64 (3.8.5-2ubuntu1) ...
(Reading database ... 15820 files and directories currently installed.)
Preparing to unpack .../archives/apt_2.9.3_amd64.deb ...
Unpacking apt (2.9.3) over (2.7.3) ...
Setting up apt (2.9.3) ...
(Reading database ... 15820 files and directories currently installed.)
Preparing to unpack .../apt-utils_2.9.3_amd64.deb ...
Unpacking apt-utils (2.9.3) over (2.7.3) ...
Preparing to unpack .../libpam-modules-bin_1.5.3-7ubuntu1_amd64.deb ...
Unpacking libpam-modules-bin (1.5.3-7ubuntu1) over (1.5.2-6ubuntu1) ...
Setting up libpam-modules-bin (1.5.3-7ubuntu1) ...
(Reading database ... 15820 files and directories currently installed.)
Preparing to unpack .../libpam-modules_1.5.3-7ubuntu1_amd64.deb ...
Unpacking libpam-modules:amd64 (1.5.3-7ubuntu1) over (1.5.2-6ubuntu1) ...
dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu/security': Directory not empty
Setting up libpam-modules:amd64 (1.5.3-7ubuntu1) ...
Installing new version of config file /etc/security/namespace.init ...
(Reading database ... 15820 files and directories currently installed.)
Preparing to unpack .../bzip2_1.0.8-5.1_amd64.deb ...
Unpacking bzip2 (1.0.8-5.1) over (1.0.8-5build1) ...
dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat')
dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2')
dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat')
dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2')
dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat')
dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2')
Preparing to unpack .../libbz2-1.0_1.0.8-5.1_amd64.deb ...
Unpacking libbz2-1.0:amd64 (1.0.8-5.1) over (1.0.8-5build1) ...
Setting up libbz2-1.0:amd64 (1.0.8-5.1) ...
Selecting previously unselected package gcc-14-base:amd64.
(Reading database ... 15820 files and directories currently installed.)
Preparing to unpack .../gcc-14-base_14-20240429-1ubuntu1_amd64.deb ...
Unpacking gcc-14-base:amd64 (14-20240429-1ubuntu1) ...
Setting up gcc-14-base:amd64 (14-20240429-1ubuntu1) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libgcc-s1_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libgcc-s1:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Setting up libgcc-s1:amd64 (14-20240429-1ubuntu1) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libgpg-error-l10n_1.49-2_all.deb ...
Unpacking libgpg-error-l10n (1.49-2) over (1.47-2) ...
Preparing to unpack .../libgpg-error0_1.49-2_amd64.deb ...
Unpacking libgpg-error0:amd64 (1.49-2) over (1.47-2) ...
Setting up libgpg-error0:amd64 (1.49-2) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libgcrypt20_1.10.3-2build1_amd64.deb ...
Unpacking libgcrypt20:amd64 (1.10.3-2build1) over (1.10.2-3ubuntu1) ...
Setting up libgcrypt20:amd64 (1.10.3-2build1) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../liblz4-1_1.9.4-2_amd64.deb ...
Unpacking liblz4-1:amd64 (1.9.4-2) over (1.9.4-1) ...
Setting up liblz4-1:amd64 (1.9.4-2) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libstdc++6_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libstdc++6:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Setting up libstdc++6:amd64 (14-20240429-1ubuntu1) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libxxhash0_0.8.2-2build1_amd64.deb ...
Unpacking libxxhash0:amd64 (0.8.2-2build1) over (0.8.1-1) ...
Setting up libxxhash0:amd64 (0.8.2-2build1) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libzstd1_1.5.5+dfsg2-2build1_amd64.deb ...
Unpacking libzstd1:amd64 (1.5.5+dfsg2-2build1) over (1.5.5+dfsg2-1ubuntu2) ...
Setting up libzstd1:amd64 (1.5.5+dfsg2-2build1) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu2_amd64.deb ...
Unpacking zlib1g:amd64 (1:1.3.dfsg-3.1ubuntu2) over (1:1.2.13.dfsg-1ubuntu5) ...
Setting up zlib1g:amd64 (1:1.3.dfsg-3.1ubuntu2) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libgmp10_2%3a6.3.0+dfsg-2ubuntu6_amd64.deb ...
Unpacking libgmp10:amd64 (2:6.3.0+dfsg-2ubuntu6) over (2:6.3.0+dfsg-2ubuntu4) ...
Setting up libgmp10:amd64 (2:6.3.0+dfsg-2ubuntu6) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libffi8_3.4.6-1build1_amd64.deb ...
Unpacking libffi8:amd64 (3.4.6-1build1) over (3.4.4-1) ...
Setting up libffi8:amd64 (3.4.6-1build1) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libidn2-0_2.3.7-2build1_amd64.deb ...
Unpacking libidn2-0:amd64 (2.3.7-2build1) over (2.3.4-1) ...
Setting up libidn2-0:amd64 (2.3.7-2build1) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libtasn1-6_4.19.0-3build1_amd64.deb ...
Unpacking libtasn1-6:amd64 (4.19.0-3build1) over (4.19.0-3) ...
Setting up libtasn1-6:amd64 (4.19.0-3build1) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libdebconfclient0_0.271ubuntu3_amd64.deb ...
Unpacking libdebconfclient0:amd64 (0.271ubuntu3) over (0.270ubuntu1) ...
Setting up libdebconfclient0:amd64 (0.271ubuntu3) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../base-passwd_3.6.3build1_amd64.deb ...
Unpacking base-passwd (3.6.3build1) over (3.6.1) ...
Setting up base-passwd (3.6.3build1) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libassuan0_2.5.6-1build1_amd64.deb ...
Unpacking libassuan0:amd64 (2.5.6-1build1) over (2.5.6-1) ...
Setting up libassuan0:amd64 (2.5.6-1build1) ...
(Reading database ... 15825 files and directories currently installed.)
Preparing to unpack .../libsqlite3-0_3.45.3-1_amd64.deb ...
Unpacking libsqlite3-0:amd64 (3.45.3-1) over (3.42.0-1) ...
Preparing to unpack .../gpg_2.4.4-2ubuntu17_amd64.deb ...
Unpacking gpg (2.4.4-2ubuntu17) over (2.2.40-1.1ubuntu1) ...
dpkg: libreadline8:amd64: dependency problems, but removing anyway as you requested:
 gpgconf depends on libreadline8 (>= 6.0).

(Reading database ... 15825 files and directories currently installed.)
Removing libreadline8:amd64 (8.2-1.3) ...
Selecting previously unselected package libreadline8t64:amd64.
(Reading database ... 15813 files and directories currently installed.)
Preparing to unpack .../libreadline8t64_8.2-4build1_amd64.deb ...
Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:amd64 (8.2-4build1) ...
Preparing to unpack .../readline-common_8.2-4build1_all.deb ...
Unpacking readline-common (8.2-4build1) over (8.2-1.3) ...
Preparing to unpack .../libncursesw6_6.4+20240113-1ubuntu2_amd64.deb ...
Unpacking libncursesw6:amd64 (6.4+20240113-1ubuntu2) over (6.4+20230625-2) ...
Preparing to unpack .../libtinfo6_6.4+20240113-1ubuntu2_amd64.deb ...
Unpacking libtinfo6:amd64 (6.4+20240113-1ubuntu2) over (6.4+20230625-2) ...
Setting up libtinfo6:amd64 (6.4+20240113-1ubuntu2) ...
(Reading database ... 15833 files and directories currently installed.)
Preparing to unpack .../gpg-agent_2.4.4-2ubuntu17_amd64.deb ...
Unpacking gpg-agent (2.4.4-2ubuntu17) over (2.2.40-1.1ubuntu1) ...
Preparing to unpack .../gpgconf_2.4.4-2ubuntu17_amd64.deb ...
Unpacking gpgconf (2.4.4-2ubuntu17) over (2.2.40-1.1ubuntu1) ...
Preparing to unpack .../pinentry-curses_1.2.1-3ubuntu5_amd64.deb ...
Unpacking pinentry-curses (1.2.1-3ubuntu5) over (1.2.1-1ubuntu1) ...
Preparing to unpack .../init-system-helpers_1.66ubuntu1_all.deb ...
Unpacking init-system-helpers (1.66ubuntu1) over (1.65.2ubuntu1) ...
Setting up init-system-helpers (1.66ubuntu1) ...
(Reading database ... 15832 files and directories currently installed.)
Removing libnpth0:amd64 (1.6-3build2) ...
Selecting previously unselected package libnpth0t64:amd64.
(Reading database ... 15827 files and directories currently installed.)
Preparing to unpack .../libnpth0t64_1.6-3.1build1_amd64.deb ...
Unpacking libnpth0t64:amd64 (1.6-3.1build1) ...
Setting up libnpth0t64:amd64 (1.6-3.1build1) ...
(Reading database ... 15833 files and directories currently installed.)
Preparing to unpack .../gpgv_2.4.4-2ubuntu17_amd64.deb ...
Unpacking gpgv (2.4.4-2ubuntu17) over (2.2.40-1.1ubuntu1) ...
Setting up gpgv (2.4.4-2ubuntu17) ...
(Reading database ... 15833 files and directories currently installed.)
Preparing to unpack .../ubuntu-keyring_2023.11.28.1_all.deb ...
Unpacking ubuntu-keyring (2023.11.28.1) over (2021.03.26) ...
Setting up ubuntu-keyring (2023.11.28.1) ...
(Reading database ... 15833 files and directories currently installed.)
Preparing to unpack .../libseccomp2_2.5.5-1ubuntu3_amd64.deb ...
Unpacking libseccomp2:amd64 (2.5.5-1ubuntu3) over (2.5.4-1ubuntu3) ...
Setting up libseccomp2:amd64 (2.5.5-1ubuntu3) ...
(Reading database ... 15833 files and directories currently installed.)
Preparing to unpack .../debconf-i18n_1.5.86ubuntu1_all.deb ...
Unpacking debconf-i18n (1.5.86ubuntu1) over (1.5.82) ...
Preparing to unpack .../debconf_1.5.86ubuntu1_all.deb ...
Unpacking debconf (1.5.86ubuntu1) over (1.5.82) ...
Setting up debconf (1.5.86ubuntu1) ...
Installing new version of config file /etc/debconf.conf ...
(Reading database ... 15832 files and directories currently installed.)
Preparing to unpack .../libpam0g_1.5.3-7ubuntu1_amd64.deb ...
Unpacking libpam0g:amd64 (1.5.3-7ubuntu1) over (1.5.2-6ubuntu1) ...
Setting up libpam0g:amd64 (1.5.3-7ubuntu1) ...
(Reading database ... 15831 files and directories currently installed.)
Preparing to unpack .../0-libfdisk1_2.39.3-9ubuntu6_amd64.deb ...
Unpacking libfdisk1:amd64 (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ...
Preparing to unpack .../1-mount_2.39.3-9ubuntu6_amd64.deb ...
Unpacking mount (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ...
Preparing to unpack .../2-libcom-err2_1.47.0-2.4~exp1ubuntu4_amd64.deb ...
Unpacking libcom-err2:amd64 (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2ubuntu1) ...
Preparing to unpack .../3-libkeyutils1_1.6.3-3build1_amd64.deb ...
Unpacking libkeyutils1:amd64 (1.6.3-3build1) over (1.6.3-2) ...
Preparing to unpack .../4-linux-libc-dev_6.8.0-31.31_amd64.deb ...
Unpacking linux-libc-dev:amd64 (6.8.0-31.31) over (6.5.0-9.9) ...
Preparing to unpack .../5-base-files_13.1ubuntu1_amd64.deb ...
Unpacking base-files (13.1ubuntu1) over (13ubuntu3) ...
Setting up base-files (13.1ubuntu1) ...
Installing new version of config file /etc/issue ...
Installing new version of config file /etc/issue.net ...
Installing new version of config file /etc/lsb-release ...
Installing new version of config file /etc/update-motd.d/10-help-text ...
(Reading database ... 15848 files and directories currently installed.)
Preparing to unpack .../debianutils_5.17build1_amd64.deb ...
Unpacking debianutils (5.17build1) over (5.8-1) ...
Setting up debianutils (5.17build1) ...
(Reading database ... 15847 files and directories currently installed.)
Preparing to unpack .../bash_5.2.21-2ubuntu4_amd64.deb ...
Unpacking bash (5.2.21-2ubuntu4) over (5.2.15-2ubuntu1) ...
Setting up bash (5.2.21-2ubuntu4) ...
update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode
(Reading database ... 15847 files and directories currently installed.)
Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu6_amd64.deb ...
Unpacking bsdutils (1:2.39.3-9ubuntu6) over (1:2.39.1-4ubuntu2) ...
Setting up bsdutils (1:2.39.3-9ubuntu6) ...
(Reading database ... 15847 files and directories currently installed.)
Removing usrmerge (35ubuntu1) ...
(Reading database ... 15821 files and directories currently installed.)
Preparing to unpack .../coreutils_9.4-3ubuntu6_amd64.deb ...
Unpacking coreutils (9.4-3ubuntu6) over (9.1-1ubuntu2) ...
Setting up coreutils (9.4-3ubuntu6) ...
(Reading database ... 15826 files and directories currently installed.)
Preparing to unpack .../tar_1.35+dfsg-3build1_amd64.deb ...
Unpacking tar (1.35+dfsg-3build1) over (1.34+dfsg-1.2ubuntu1) ...
Setting up tar (1.35+dfsg-3build1) ...
(Reading database ... 15826 files and directories currently installed.)
Preparing to unpack .../dpkg_1.22.6ubuntu10_amd64.deb ...
Unpacking dpkg (1.22.6ubuntu10) over (1.22.0ubuntu1) ...
Setting up dpkg (1.22.6ubuntu10) ...
(Reading database ... 15824 files and directories currently installed.)
Preparing to unpack .../dash_0.5.12-6ubuntu5_amd64.deb ...
Unpacking dash (0.5.12-6ubuntu5) over (0.5.12-6ubuntu1) ...
Setting up dash (0.5.12-6ubuntu5) ...
(Reading database ... 15823 files and directories currently installed.)
Preparing to unpack .../diffutils_1%3a3.10-1build1_amd64.deb ...
Unpacking diffutils (1:3.10-1build1) over (1:3.8-4) ...
Setting up diffutils (1:3.10-1build1) ...
(Reading database ... 15823 files and directories currently installed.)
Preparing to unpack .../findutils_4.9.0-5build1_amd64.deb ...
Unpacking findutils (4.9.0-5build1) over (4.9.0-5) ...
Setting up findutils (4.9.0-5build1) ...
(Reading database ... 15822 files and directories currently installed.)
Preparing to unpack .../grep_3.11-4build1_amd64.deb ...
Unpacking grep (3.11-4build1) over (3.11-2) ...
Setting up grep (3.11-4build1) ...
(Reading database ... 15822 files and directories currently installed.)
Preparing to unpack .../gzip_1.12-1ubuntu3_amd64.deb ...
Unpacking gzip (1.12-1ubuntu3) over (1.12-1ubuntu1) ...
dpkg: warning: old file '/bin/uncompress' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress')
dpkg: warning: old file '/bin/gunzip' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress')
Setting up gzip (1.12-1ubuntu3) ...
(Reading database ... 15822 files and directories currently installed.)
Preparing to unpack .../hostname_3.23+nmu2ubuntu2_amd64.deb ...
Unpacking hostname (3.23+nmu2ubuntu2) over (3.23+nmu1ubuntu1) ...
Setting up hostname (3.23+nmu2ubuntu2) ...
(Reading database ... 15822 files and directories currently installed.)
Preparing to unpack .../login_1%3a4.13+dfsg1-4ubuntu3_amd64.deb ...
Unpacking login (1:4.13+dfsg1-4ubuntu3) over (1:4.13+dfsg1-1ubuntu1) ...
Setting up login (1:4.13+dfsg1-4ubuntu3) ...
Installing new version of config file /etc/login.defs ...
Installing new version of config file /etc/pam.d/login ...
(Reading database ... 15822 files and directories currently installed.)
Preparing to unpack .../ncurses-bin_6.4+20240113-1ubuntu2_amd64.deb ...
Unpacking ncurses-bin (6.4+20240113-1ubuntu2) over (6.4+20230625-2) ...
Setting up ncurses-bin (6.4+20240113-1ubuntu2) ...
(Reading database ... 15822 files and directories currently installed.)
Preparing to unpack .../sed_4.9-2build1_amd64.deb ...
Unpacking sed (4.9-2build1) over (4.9-1) ...
Setting up sed (4.9-2build1) ...
(Reading database ... 15822 files and directories currently installed.)
Preparing to unpack .../util-linux_2.39.3-9ubuntu6_amd64.deb ...
Unpacking util-linux (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ...
Setting up util-linux (2.39.3-9ubuntu6) ...
(Reading database ... 15824 files and directories currently installed.)
Preparing to unpack .../ncurses-base_6.4+20240113-1ubuntu2_all.deb ...
Unpacking ncurses-base (6.4+20240113-1ubuntu2) over (6.4+20230625-2) ...
Setting up ncurses-base (6.4+20240113-1ubuntu2) ...
(Reading database ... 15824 files and directories currently installed.)
Preparing to unpack .../sysvinit-utils_3.08-6ubuntu3_amd64.deb ...
Unpacking sysvinit-utils (3.08-6ubuntu3) over (3.07-1ubuntu1) ...
dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty
dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty
dpkg: warning: unable to delete old directory '/lib/init': Directory not empty
Setting up sysvinit-utils (3.08-6ubuntu3) ...
(Reading database ... 15822 files and directories currently installed.)
Preparing to unpack .../logsave_1.47.0-2.4~exp1ubuntu4_amd64.deb ...
Unpacking logsave (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2ubuntu1) ...
dpkg: libext2fs2:amd64: dependency problems, but removing anyway as you requested:
 e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1).

(Reading database ... 15822 files and directories currently installed.)
Removing libext2fs2:amd64 (1.47.0-2ubuntu1) ...
Selecting previously unselected package libext2fs2t64:amd64.
(Reading database ... 15815 files and directories currently installed.)
Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu4_amd64.deb ...
Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64'
Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64'
Unpacking libext2fs2t64:amd64 (1.47.0-2.4~exp1ubuntu4) ...
Setting up libcom-err2:amd64 (1.47.0-2.4~exp1ubuntu4) ...
Setting up libext2fs2t64:amd64 (1.47.0-2.4~exp1ubuntu4) ...
(Reading database ... 15831 files and directories currently installed.)
Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu4_amd64.deb ...
Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2ubuntu1) ...
dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty
dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty
Preparing to unpack .../optipng_0.7.8+ds-1build2_amd64.deb ...
Unpacking optipng (0.7.8+ds-1build2) over (0.7.7-2build1) ...
(Reading database ... 15829 files and directories currently installed.)
Removing libpng16-16:amd64 (1.6.40-1) ...
Selecting previously unselected package libpng16-16t64:amd64.
(Reading database ... 15819 files and directories currently installed.)
Preparing to unpack .../libpng16-16t64_1.6.43-5build1_amd64.deb ...
Unpacking libpng16-16t64:amd64 (1.6.43-5build1) ...
Setting up libapparmor1:amd64 (4.0.1-0ubuntu1) ...
Setting up libargon2-1:amd64 (0~20190702+dfsg-4build1) ...
Setting up libdevmapper1.02.1:amd64 (2:1.02.185-3ubuntu3) ...
Setting up libjson-c5:amd64 (0.17-1build1) ...
Setting up libcryptsetup12:amd64 (2:2.7.0-1ubuntu4) ...
Setting up libfdisk1:amd64 (2.39.3-9ubuntu6) ...
Setting up libsystemd-shared:amd64 (256~rc1-1~exp2ubuntu1) ...
Setting up systemd-dev (256~rc1-1~exp2ubuntu1) ...
Setting up mount (2.39.3-9ubuntu6) ...
Setting up systemd (256~rc1-1~exp2ubuntu1) ...
Installing new version of config file /etc/systemd/journald.conf ...
Installing new version of config file /etc/systemd/logind.conf ...
Installing new version of config file /etc/systemd/networkd.conf ...
Installing new version of config file /etc/systemd/pstore.conf ...
Installing new version of config file /etc/systemd/sleep.conf ...
Installing new version of config file /etc/systemd/system.conf ...
Installing new version of config file /etc/systemd/user.conf ...
Initializing machine ID from random generator.
Setting up systemd-sysv (256~rc1-1~exp2ubuntu1) ...
(Reading database ... 15830 files and directories currently installed.)
Preparing to unpack .../init_1.66ubuntu1_amd64.deb ...
Unpacking init (1.66ubuntu1) over (1.65.2ubuntu1) ...
Preparing to unpack .../libsmartcols1_2.39.3-9ubuntu6_amd64.deb ...
Unpacking libsmartcols1:amd64 (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ...
Setting up libsmartcols1:amd64 (2.39.3-9ubuntu6) ...
(Reading database ... 15831 files and directories currently installed.)
Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu6_amd64.deb ...
Unpacking uuid-runtime (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ...
dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty
Preparing to unpack .../libattr1_1%3a2.5.2-1build1_amd64.deb ...
Unpacking libattr1:amd64 (1:2.5.2-1build1) over (1:2.5.1-4) ...
Setting up libattr1:amd64 (1:2.5.2-1build1) ...
(Reading database ... 15829 files and directories currently installed.)
Preparing to unpack .../libmd0_1.1.0-2build1_amd64.deb ...
Unpacking libmd0:amd64 (1.1.0-2build1) over (1.1.0-1) ...
Setting up libmd0:amd64 (1.1.0-2build1) ...
(Reading database ... 15829 files and directories currently installed.)
Preparing to unpack .../libpam-runtime_1.5.3-7ubuntu1_all.deb ...
Unpacking libpam-runtime (1.5.3-7ubuntu1) over (1.5.2-6ubuntu1) ...
Setting up libpam-runtime (1.5.3-7ubuntu1) ...
(Reading database ... 15828 files and directories currently installed.)
Preparing to unpack .../libsemanage-common_3.5-1build5_all.deb ...
Unpacking libsemanage-common (3.5-1build5) over (3.5-1) ...
Setting up libsemanage-common (3.5-1build5) ...
(Reading database ... 15828 files and directories currently installed.)
Preparing to unpack .../libsepol2_3.5-2build1_amd64.deb ...
Unpacking libsepol2:amd64 (3.5-2build1) over (3.5-1) ...
Setting up libsepol2:amd64 (3.5-2build1) ...
(Reading database ... 15828 files and directories currently installed.)
Preparing to unpack .../libsemanage2_3.5-1build5_amd64.deb ...
Unpacking libsemanage2:amd64 (3.5-1build5) over (3.5-1) ...
Setting up libsemanage2:amd64 (3.5-1build5) ...
(Reading database ... 15828 files and directories currently installed.)
Preparing to unpack .../passwd_1%3a4.13+dfsg1-4ubuntu3_amd64.deb ...
Unpacking passwd (1:4.13+dfsg1-4ubuntu3) over (1:4.13+dfsg1-1ubuntu1) ...
Setting up passwd (1:4.13+dfsg1-4ubuntu3) ...
(Reading database ... 15828 files and directories currently installed.)
Preparing to unpack .../00-libproc2-0_2%3a4.0.4-4ubuntu3_amd64.deb ...
Unpacking libproc2-0:amd64 (2:4.0.4-4ubuntu3) over (2:4.0.3-1ubuntu1) ...
Preparing to unpack .../01-libss2_1.47.0-2.4~exp1ubuntu4_amd64.deb ...
Unpacking libss2:amd64 (1.47.0-2.4~exp1ubuntu4) over (1.47.0-2ubuntu1) ...
Preparing to unpack .../02-mawk_1.3.4.20240123-1build1_amd64.deb ...
Unpacking mawk (1.3.4.20240123-1build1) over (1.3.4.20230730-1) ...
Preparing to unpack .../03-procps_2%3a4.0.4-4ubuntu3_amd64.deb ...
Unpacking procps (2:4.0.4-4ubuntu3) over (2:4.0.3-1ubuntu1) ...
Preparing to unpack .../04-sensible-utils_0.0.22_all.deb ...
Unpacking sensible-utils (0.0.22) over (0.0.20) ...
Preparing to unpack .../05-ca-certificates_20240203_all.deb ...
Unpacking ca-certificates (20240203) over (20230311ubuntu1) ...
Preparing to unpack .../06-krb5-locales_1.20.1-6ubuntu2_all.deb ...
Unpacking krb5-locales (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ...
Preparing to unpack .../07-tzdata_2024a-4ubuntu1_all.deb ...
Unpacking tzdata (2024a-4ubuntu1) over (2023c-9ubuntu1) ...
Preparing to unpack .../08-bash-completion_1%3a2.13.0-1_all.deb ...
Unpacking bash-completion (1:2.13.0-1) over (1:2.11-7) ...
Preparing to unpack .../09-bsdextrautils_2.39.3-9ubuntu6_amd64.deb ...
Unpacking bsdextrautils (2.39.3-9ubuntu6) over (2.39.1-4ubuntu2) ...
Preparing to unpack .../10-libgpm2_1.20.7-11_amd64.deb ...
Unpacking libgpm2:amd64 (1.20.7-11) over (1.20.7-10build1) ...
Preparing to unpack .../11-libip4tc2_1.8.10-3ubuntu2_amd64.deb ...
Unpacking libip4tc2:amd64 (1.8.10-3ubuntu2) over (1.8.9-2ubuntu2) ...
Preparing to unpack .../12-libjansson4_2.14-2build2_amd64.deb ...
Unpacking libjansson4:amd64 (2.14-2build2) over (2.14-2) ...
Preparing to unpack .../13-psmisc_23.7-1build1_amd64.deb ...
Unpacking psmisc (23.7-1build1) over (23.6-1) ...
Preparing to unpack .../14-xz-utils_5.6.1+really5.4.5-1_amd64.deb ...
Unpacking xz-utils (5.6.1+really5.4.5-1) over (5.4.1-0.2) ...
Preparing to unpack .../15-advancecomp_2.5-1build1_amd64.deb ...
Unpacking advancecomp (2.5-1build1) over (2.5-1) ...
Preparing to unpack .../16-libgprofng0_2.42-4ubuntu2_amd64.deb ...
Unpacking libgprofng0:amd64 (2.42-4ubuntu2) over (2.41-5ubuntu1) ...
Preparing to unpack .../17-libctf0_2.42-4ubuntu2_amd64.deb ...
Unpacking libctf0:amd64 (2.42-4ubuntu2) over (2.41-5ubuntu1) ...
Preparing to unpack .../18-libctf-nobfd0_2.42-4ubuntu2_amd64.deb ...
Unpacking libctf-nobfd0:amd64 (2.42-4ubuntu2) over (2.41-5ubuntu1) ...
Preparing to unpack .../19-binutils-x86-64-linux-gnu_2.42-4ubuntu2_amd64.deb ...
Unpacking binutils-x86-64-linux-gnu (2.42-4ubuntu2) over (2.41-5ubuntu1) ...
Preparing to unpack .../20-libbinutils_2.42-4ubuntu2_amd64.deb ...
Unpacking libbinutils:amd64 (2.42-4ubuntu2) over (2.41-5ubuntu1) ...
Preparing to unpack .../21-binutils_2.42-4ubuntu2_amd64.deb ...
Unpacking binutils (2.42-4ubuntu2) over (2.41-5ubuntu1) ...
Preparing to unpack .../22-binutils-common_2.42-4ubuntu2_amd64.deb ...
Unpacking binutils-common:amd64 (2.42-4ubuntu2) over (2.41-5ubuntu1) ...
Preparing to unpack .../23-libsframe1_2.42-4ubuntu2_amd64.deb ...
Unpacking libsframe1:amd64 (2.42-4ubuntu2) over (2.41-5ubuntu1) ...
Preparing to unpack .../24-libubsan1_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libubsan1:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../25-g++-13_13.2.0-25ubuntu1_amd64.deb ...
Unpacking g++-13 (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../26-libstdc++-13-dev_13.2.0-25ubuntu1_amd64.deb ...
Unpacking libstdc++-13-dev:amd64 (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../27-libgomp1_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libgomp1:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../28-libitm1_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libitm1:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../29-libatomic1_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libatomic1:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../30-libasan8_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libasan8:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../31-liblsan0_14-20240429-1ubuntu1_amd64.deb ...
Unpacking liblsan0:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../32-libhwasan0_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libhwasan0:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../33-libquadmath0_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libquadmath0:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../34-gcc-13_13.2.0-25ubuntu1_amd64.deb ...
Unpacking gcc-13 (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../35-libgcc-13-dev_13.2.0-25ubuntu1_amd64.deb ...
Unpacking libgcc-13-dev:amd64 (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../36-libtsan2_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libtsan2:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../37-libcc1-0_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libcc1-0:amd64 (14-20240429-1ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../38-cpp-13_13.2.0-25ubuntu1_amd64.deb ...
Unpacking cpp-13 (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../39-gcc-13-base_13.2.0-25ubuntu1_amd64.deb ...
Unpacking gcc-13-base:amd64 (13.2.0-25ubuntu1) over (13.2.0-4ubuntu3) ...
Preparing to unpack .../40-libisl23_0.26-3build1_amd64.deb ...
Unpacking libisl23:amd64 (0.26-3build1) over (0.26-3) ...
Preparing to unpack .../41-libmpfr6_4.2.1-1build1_amd64.deb ...
Unpacking libmpfr6:amd64 (4.2.1-1build1) over (4.2.1-1) ...
Preparing to unpack .../42-libmpc3_1.3.1-1build1_amd64.deb ...
Unpacking libmpc3:amd64 (1.3.1-1build1) over (1.3.1-1) ...
Selecting previously unselected package gcc-13-x86-64-linux-gnu.
Preparing to unpack .../43-gcc-13-x86-64-linux-gnu_13.2.0-25ubuntu1_amd64.deb ...
Unpacking gcc-13-x86-64-linux-gnu (13.2.0-25ubuntu1) ...
Selecting previously unselected package g++-13-x86-64-linux-gnu.
Preparing to unpack .../44-g++-13-x86-64-linux-gnu_13.2.0-25ubuntu1_amd64.deb ...
Unpacking g++-13-x86-64-linux-gnu (13.2.0-25ubuntu1) ...
Selecting previously unselected package cpp-13-x86-64-linux-gnu.
Preparing to unpack .../45-cpp-13-x86-64-linux-gnu_13.2.0-25ubuntu1_amd64.deb ...
Unpacking cpp-13-x86-64-linux-gnu (13.2.0-25ubuntu1) ...
Preparing to unpack .../46-g++_4%3a13.2.0-7ubuntu1_amd64.deb ...
Unpacking g++ (4:13.2.0-7ubuntu1) over (4:13.2.0-1ubuntu1) ...
Preparing to unpack .../47-gcc_4%3a13.2.0-7ubuntu1_amd64.deb ...
Unpacking gcc (4:13.2.0-7ubuntu1) over (4:13.2.0-1ubuntu1) ...
Preparing to unpack .../48-cpp_4%3a13.2.0-7ubuntu1_amd64.deb ...
Unpacking cpp (4:13.2.0-7ubuntu1) over (4:13.2.0-1ubuntu1) ...
Selecting previously unselected package cpp-x86-64-linux-gnu.
Preparing to unpack .../49-cpp-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
Unpacking cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
Selecting previously unselected package gcc-x86-64-linux-gnu.
Preparing to unpack .../50-gcc-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
Unpacking gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
Selecting previously unselected package g++-x86-64-linux-gnu.
Preparing to unpack .../51-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ...
Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
Preparing to unpack .../52-dpkg-dev_1.22.6ubuntu10_all.deb ...
Unpacking dpkg-dev (1.22.6ubuntu10) over (1.22.0ubuntu1) ...
Preparing to unpack .../53-libdpkg-perl_1.22.6ubuntu10_all.deb ...
Unpacking libdpkg-perl (1.22.6ubuntu10) over (1.22.0ubuntu1) ...
Preparing to unpack .../54-patch_2.7.6-7build3_amd64.deb ...
Unpacking patch (2.7.6-7build3) over (2.7.6-7build2) ...
Preparing to unpack .../55-make_4.3-4.1build2_amd64.deb ...
Unpacking make (4.3-4.1build2) over (4.3-4.1build1) ...
Preparing to unpack .../56-lto-disabled-list_48_all.deb ...
Unpacking lto-disabled-list (48) over (43) ...
Preparing to unpack .../57-libfakeroot_1.34-1_amd64.deb ...
Unpacking libfakeroot:amd64 (1.34-1) over (1.32.1-1) ...
Preparing to unpack .../58-fakeroot_1.34-1_amd64.deb ...
Unpacking fakeroot (1.34-1) over (1.32.1-1) ...
Preparing to unpack .../59-liblockfile-bin_1.17-1build3_amd64.deb ...
Unpacking liblockfile-bin (1.17-1build3) over (1.17-1build2) ...
Preparing to unpack .../60-liblockfile1_1.17-1build3_amd64.deb ...
Unpacking liblockfile1:amd64 (1.17-1build3) over (1.17-1build2) ...
Preparing to unpack .../61-lockfile-progs_0.1.19+nmu1_amd64.deb ...
Unpacking lockfile-progs (0.1.19+nmu1) over (0.1.19build1) ...
Setting up libip4tc2:amd64 (1.8.10-3ubuntu2) ...
Setting up libtext-iconv-perl:amd64 (1.7-8build3) ...
Setting up libtext-charwidth-perl:amd64 (0.04-11build3) ...
Setting up libkeyutils1:amd64 (1.6.3-3build1) ...
Setting up lto-disabled-list (48) ...
Setting up apt-utils (2.9.3) ...
Setting up libgpm2:amd64 (1.20.7-11) ...
Setting up liblockfile-bin (1.17-1build3) ...
Setting up libgdbm6t64:amd64 (1.23-5.1build1) ...
Setting up bsdextrautils (2.39.3-9ubuntu6) ...
Setting up init (1.66ubuntu1) ...
Setting up libgdbm-compat4t64:amd64 (1.23-5.1build1) ...
Setting up psmisc (23.7-1build1) ...
Setting up libtirpc-common (1.3.4+ds-1.3) ...
Setting up libsqlite3-0:amd64 (3.45.3-1) ...
Setting up binutils-common:amd64 (2.42-4ubuntu2) ...
Installing new version of config file /etc/gprofng.rc ...
Setting up linux-libc-dev:amd64 (6.8.0-31.31) ...
Setting up libctf-nobfd0:amd64 (2.42-4ubuntu2) ...
Setting up krb5-locales (1.20.1-6ubuntu2) ...
Setting up libgomp1:amd64 (14-20240429-1ubuntu1) ...
Setting up bzip2 (1.0.8-5.1) ...
Setting up libsframe1:amd64 (2.42-4ubuntu2) ...
Setting up libfakeroot:amd64 (1.34-1) ...
Setting up libjansson4:amd64 (2.14-2build2) ...
Setting up libkrb5support0:amd64 (1.20.1-6ubuntu2) ...
Setting up tzdata (2024a-4ubuntu1) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Tue May 14 23:17:23 UTC 2024.
Universal Time is now:  Tue May 14 23:17:23 UTC 2024.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up fakeroot (1.34-1) ...
Setting up rpcsvc-proto (1.4.2-0ubuntu7) ...
Setting up gcc-13-base:amd64 (13.2.0-25ubuntu1) ...
Setting up make (4.3-4.1build2) ...
Setting up libmpfr6:amd64 (4.2.1-1build1) ...
Setting up bash-completion (1:2.13.0-1) ...
Installing new version of config file /etc/profile.d/bash_completion.sh ...
Setting up xz-utils (5.6.1+really5.4.5-1) ...
Setting up perl-modules-5.38 (5.38.2-4) ...
Setting up libquadmath0:amd64 (14-20240429-1ubuntu1) ...
Setting up libproc2-0:amd64 (2:4.0.4-4ubuntu3) ...
Setting up libpng16-16t64:amd64 (1.6.43-5build1) ...
Setting up libmpc3:amd64 (1.3.1-1build1) ...
Setting up libatomic1:amd64 (14-20240429-1ubuntu1) ...
Setting up patch (2.7.6-7build3) ...
Setting up libss2:amd64 (1.47.0-2.4~exp1ubuntu4) ...
Setting up libncursesw6:amd64 (6.4+20240113-1ubuntu2) ...
Setting up libk5crypto3:amd64 (1.20.1-6ubuntu2) ...
Setting up logsave (1.47.0-2.4~exp1ubuntu4) ...
Setting up libubsan1:amd64 (14-20240429-1ubuntu1) ...
Setting up advancecomp (2.5-1build1) ...
Setting up sensible-utils (0.0.22) ...
Setting up uuid-runtime (2.39.3-9ubuntu6) ...
Running in chroot, ignoring request.
invoke-rc.d: policy-rc.d denied execution of restart.
Setting up libhwasan0:amd64 (14-20240429-1ubuntu1) ...
Setting up libcrypt-dev:amd64 (1:4.4.36-4build1) ...
Setting up libasan8:amd64 (14-20240429-1ubuntu1) ...
Setting up procps (2:4.0.4-4ubuntu3) ...
Installing new version of config file /etc/sysctl.conf ...
Setting up mawk (1.3.4.20240123-1build1) ...
Setting up libkrb5-3:amd64 (1.20.1-6ubuntu2) ...
Setting up liblockfile1:amd64 (1.17-1build3) ...
Setting up libperl5.38t64:amd64 (5.38.2-4) ...
Setting up libtsan2:amd64 (14-20240429-1ubuntu1) ...
Setting up libbinutils:amd64 (2.42-4ubuntu2) ...
Setting up libisl23:amd64 (0.26-3build1) ...
Setting up libc-dev-bin (2.39-0ubuntu8.1) ...
Setting up openssl (3.0.13-0ubuntu3) ...
Setting up libgpg-error-l10n (1.49-2) ...
Setting up readline-common (8.2-4build1) ...
Setting up libcc1-0:amd64 (14-20240429-1ubuntu1) ...
Setting up liblocale-gettext-perl (1.07-7) ...
Setting up liblsan0:amd64 (14-20240429-1ubuntu1) ...
Setting up libitm1:amd64 (14-20240429-1ubuntu1) ...
Setting up libkmod2:amd64 (31+20240202-2ubuntu7) ...
Setting up libctf0:amd64 (2.42-4ubuntu2) ...
Setting up pinentry-curses (1.2.1-3ubuntu5) ...
Setting up cpp-13-x86-64-linux-gnu (13.2.0-25ubuntu1) ...
Setting up debconf-i18n (1.5.86ubuntu1) ...
Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ...
Setting up ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL
14 added, 5 removed; done.
Setting up perl (5.38.2-4) ...
Setting up libgprofng0:amd64 (2.42-4ubuntu2) ...
Setting up optipng (0.7.8+ds-1build2) ...
Setting up lockfile-progs (0.1.19+nmu1) ...
Setting up libgssapi-krb5-2:amd64 (1.20.1-6ubuntu2) ...
Setting up libdpkg-perl (1.22.6ubuntu10) ...
Setting up libreadline8t64:amd64 (8.2-4build1) ...
Setting up libgcc-13-dev:amd64 (13.2.0-25ubuntu1) ...
Setting up gpgconf (2.4.4-2ubuntu17) ...
Setting up libc6-dev:amd64 (2.39-0ubuntu8.1) ...
Setting up gpg (2.4.4-2ubuntu17) ...
Setting up libstdc++-13-dev:amd64 (13.2.0-25ubuntu1) ...
Setting up binutils-x86-64-linux-gnu (2.42-4ubuntu2) ...
Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
Setting up gpg-agent (2.4.4-2ubuntu17) ...
Setting up cpp-13 (13.2.0-25ubuntu1) ...
Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ...
Setting up gcc-13-x86-64-linux-gnu (13.2.0-25ubuntu1) ...
Setting up binutils (2.42-4ubuntu2) ...
Setting up dpkg-dev (1.22.6ubuntu10) ...
Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3) ...
Setting up gcc-13 (13.2.0-25ubuntu1) ...
Setting up cpp (4:13.2.0-7ubuntu1) ...
Setting up libnsl2:amd64 (1.3.0-3build3) ...
Setting up g++-13-x86-64-linux-gnu (13.2.0-25ubuntu1) ...
Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
Setting up libnss-nisplus:amd64 (1.3-5build1) ...
Setting up gcc (4:13.2.0-7ubuntu1) ...
Setting up libnss-nis:amd64 (3.1-0ubuntu7) ...
Setting up libnsl-dev:amd64 (1.3.0-3build3) ...
Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ...
Setting up g++-13 (13.2.0-25ubuntu1) ...
Setting up g++ (4:13.2.0-7ubuntu1) ...
Processing triggers for libc-bin (2.39-0ubuntu8.1) ...
Processing triggers for debianutils (5.17build1) ...
(Reading database ... 16045 files and directories currently installed.)
Purging configuration files for libssl3:amd64 (3.0.10-1ubuntu2) ...
Processing triggers for ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-28446411 amd64 oracular-proposed -c chroot:build-PACKAGEBUILD-28446411 --arch=amd64 --dist=oracular-proposed --nolog -A libgoby-java_3.3.1+dfsg2-11.dsc
Initiating build PACKAGEBUILD-28446411 with 4 jobs across 4 processor cores.
Kernel reported to sbuild: 5.4.0-182-generic #202-Ubuntu SMP Fri Apr 26 12:29:36 UTC 2024 x86_64
sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-047.buildd

+==============================================================================+
| libgoby-java 3.3.1+dfsg2-11 (amd64)          Tue, 14 May 2024 23:17:28 +0000 |
+==============================================================================+

Package: libgoby-java
Version: 3.3.1+dfsg2-11
Source Version: 3.3.1+dfsg2-11
Distribution: oracular-proposed
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: binary

I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28446411/chroot-autobuild' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/libgoby-java-wvPHe8/resolver-houXkX' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Local sources
-------------

libgoby-java_3.3.1+dfsg2-11.dsc exists in .; copying to chroot
I: NOTICE: Log filtering will replace 'build/libgoby-java-wvPHe8/libgoby-java-3.3.1+dfsg2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/libgoby-java-wvPHe8' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), maven-debian-helper, javahelper, default-jdk, build-essential, fakeroot, ant, ant-contrib, libjbzip2-java, libcommons-collections3-java, libcommons-configuration-java, libcommons-exec-java, libcommons-io-java, libcommons-lang-java, libcommons-logging-java, libcommons-math-java, libcommons-cli-java, libdistlib-java, liblog4j1.2-java, libexec-maven-plugin-java, libjaxb-api-java, libmaven-assembly-plugin-java, libmaven-antrun-plugin-java, libbuild-helper-maven-plugin-java, libmaven-dependency-plugin-java, libmaven-source-plugin-java, libmaven-javadoc-plugin-java, libprotobuf-java, libhtsjdk-java, libfastutil-java, protobuf-compiler, libjsap-java, libdsiutils-java, libicb-utils-java, libreflections-java, libpj-java, libprotobuf-dev, pkgconf, r-cran-rjava, libeasymock-java, junit4, testng, libpicard-java
Filtered Build-Depends: debhelper-compat (= 13), maven-debian-helper, javahelper, default-jdk, build-essential, fakeroot, ant, ant-contrib, libjbzip2-java, libcommons-collections3-java, libcommons-configuration-java, libcommons-exec-java, libcommons-io-java, libcommons-lang-java, libcommons-logging-java, libcommons-math-java, libcommons-cli-java, libdistlib-java, liblog4j1.2-java, libexec-maven-plugin-java, libjaxb-api-java, libmaven-assembly-plugin-java, libmaven-antrun-plugin-java, libbuild-helper-maven-plugin-java, libmaven-dependency-plugin-java, libmaven-source-plugin-java, libmaven-javadoc-plugin-java, libprotobuf-java, libhtsjdk-java, libfastutil-java, protobuf-compiler, libjsap-java, libdsiutils-java, libicb-utils-java, libreflections-java, libpj-java, libprotobuf-dev, pkgconf, r-cran-rjava, libeasymock-java, junit4, testng, libpicard-java
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [963 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [659 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [724 B]
Fetched 2346 B in 0s (182 kB/s)
Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  apt-utils bash-completion debconf-i18n krb5-locales libgpg-error-l10n
  libgpm2 libip4tc2 libkmod2 liblocale-gettext-perl libnsl-dev libnsl2
  libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl
  libtext-iconv-perl libtext-wrapi18n-perl libtirpc-dev libunistring2
  perl-modules-5.36 psmisc uuid-runtime
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  adwaita-icon-theme ant ant-contrib at-spi2-common autoconf automake
  autopoint autotools-dev binfmt-support ca-certificates-java dbus dbus-bin
  dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session
  dconf-gsettings-backend dconf-service dctrl-tools debhelper debugedit
  default-jdk default-jdk-headless default-jre default-jre-headless devscripts
  dh-autoreconf dh-strip-nondeterminism dirmngr dwz fastjar file fontconfig
  fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base
  gnupg gnupg-utils gpgsm groff-base gtk-update-icon-cache hicolor-icon-theme
  humanity-icon-theme intltool-debian jarwrapper java-common java-wrappers
  javahelper junit4 junit5 keyboxd libactivation-java libaopalliance-java
  libapache-pom-java libapiguardian-java libarchive-zip-perl libasm-java
  libasound2-data libasound2t64 libatinject-jsr330-api-java
  libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3
  libavahi-common-data libavahi-common3 libb-hooks-op-check-perl
  libbarclay-java libbatik-java libblas3 libbrotli1 libbsd0 libbsh-java
  libbuild-helper-maven-plugin-java libbyte-buddy-java libcairo-gobject2
  libcairo2 libcdi-api-java libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libcolord2 libcolt-free-java
  libcommons-beanutils-java libcommons-cli-java libcommons-codec-java
  libcommons-collections3-java libcommons-collections4-java
  libcommons-compress-java libcommons-configuration-java
  libcommons-digester-java libcommons-exec-java libcommons-io-java
  libcommons-jexl2-java libcommons-lang-java libcommons-lang3-java
  libcommons-logging-java libcommons-math-java libcommons-math3-java
  libcommons-parent-java libcommons-text-java libcommons-validator-java
  libcups2t64 libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdebhelper-perl
  libdeflate0 libdevel-callchecker-perl libdistlib-java libdom4j-java
  libdoxia-core-java libdoxia-java libdoxia-sitetools-java libdrm-amdgpu1
  libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2
  libdsiutils-java libdw1t64 libdynaloader-functions-perl libeasymock-java
  libedit2 libel-api-java libelf1t64 libencode-locale-perl libepoxy0
  liberror-prone-java libexec-maven-plugin-java libexpat1 libfastutil-java
  libfile-dirlist-perl libfile-homedir-perl libfile-listing-perl
  libfile-stripnondeterminism-perl libfile-touch-perl libfile-which-perl
  libfontbox2-java libfontconfig1 libfop-java libfreemarker-java libfreetype6
  libfribidi0 libgatk-native-bindings-java libgdk-pixbuf-2.0-0
  libgdk-pixbuf2.0-common libgeronimo-annotation-1.3-spec-java
  libgeronimo-interceptor-3.0-spec-java libgfortran5 libgif7 libgkl-java
  libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0
  libglx0 libgoogle-gson-java libgraphite2-3 libgtk-3-0t64 libgtk-3-common
  libguava-java libguice-java libhamcrest-java libharfbuzz0b
  libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhtsjdk-java
  libhttp-cookies-perl libhttp-date-perl libhttp-message-perl
  libhttp-negotiate-perl libhttpclient-java libhttpcore-java libicb-utils-java
  libice6 libicu4j-java libicu74 libimport-into-perl libio-html-perl
  libio-pty-perl libio-socket-ssl-perl libipc-run-perl libitext1-java
  libjansi-java libjavassist-java libjaxb-api-java libjaxen-java
  libjaxp1.3-java libjbig0 libjboss-logging-java libjboss-vfs-java
  libjbzip2-java libjcommander-java libjetty9-java libjoptsimple-java
  libjpeg-turbo8 libjpeg8 libjsap-java libjsoup-java libjsp-api-java
  libjsr305-java libjtidy-java libksba8 liblapack3 liblcms2-2 libldap2
  liblerc4 liblightcouch-java libllvm17t64 liblog4j1.2-java liblog4j2-java
  liblogback-java liblwp-mediatypes-perl liblwp-protocol-https-perl
  libmagic-mgc libmagic1t64 libmaven-antrun-plugin-java libmaven-archiver-java
  libmaven-artifact-transfer-java libmaven-assembly-plugin-java
  libmaven-clean-plugin-java libmaven-common-artifact-filters-java
  libmaven-compiler-plugin-java libmaven-dependency-analyzer-java
  libmaven-dependency-plugin-java libmaven-dependency-tree-java
  libmaven-file-management-java libmaven-filtering-java libmaven-invoker-java
  libmaven-jar-plugin-java libmaven-javadoc-plugin-java libmaven-parent-java
  libmaven-plugin-tools-java libmaven-reporting-api-java
  libmaven-reporting-exec-java libmaven-reporting-impl-java
  libmaven-resolver-java libmaven-resources-plugin-java
  libmaven-shared-incremental-java libmaven-shared-io-java
  libmaven-shared-utils-java libmaven-site-plugin-java
  libmaven-source-plugin-java libmaven3-core-java libmbedcrypto7t64
  libmbedtls14t64 libmbedx509-1t64 libmjson-java libmodule-runtime-perl
  libmongodb-java libmoo-perl libncbi-ngs3 libncbi-vdb3 libnet-http-perl
  libnet-ssleay-perl libnghttp2-14 libngs-java libngs-jni libnspr4 libnss3
  libobjenesis-java libopentest4j-java libopentest4j-reporting-java
  liboro-java libpam-systemd libpango-1.0-0 libpangocairo-1.0-0
  libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl
  libpciaccess0 libpcsclite1 libpicard-java libpicocli-java libpipeline1
  libpixman-1-0 libpj-java libpkgconf3 libplexus-ant-factory-java
  libplexus-archiver-java libplexus-bsh-factory-java libplexus-build-api-java
  libplexus-cipher-java libplexus-classworlds-java libplexus-compiler-java
  libplexus-component-annotations-java libplexus-container-default-java
  libplexus-container-default1.5-java libplexus-i18n-java
  libplexus-interactivity-api-java libplexus-interpolation-java
  libplexus-io-java libplexus-languages-java libplexus-sec-dispatcher-java
  libplexus-utils2-java libplexus-velocity-java libprotobuf-dev
  libprotobuf-java libprotobuf-lite32t64 libprotobuf32t64 libprotoc32t64
  libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib
  libqdox-java libqdox2-java libreflections-java librhino-java
  librole-tiny-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config
  libsensors5 libservlet-api-java libsharpyuv0 libsisu-inject-java
  libsisu-plexus-java libslf4j-java libsm6 libsnappy-java libsnappy-jni
  libsnappy1v5 libssh-4 libsub-override-perl libsub-quote-perl
  libsurefire-java libtcl8.6 libthai-data libthai0 libtiff6 libtimedate-perl
  libtk8.6 libtool libtry-tiny-perl libuchardet0 libunivocity-parsers-java
  liburi-perl libvelocity-tools-java libvulkan1 libwagon-file-java
  libwagon-http-shaded-java libwagon-provider-api-java libwayland-client0
  libwayland-cursor0 libwayland-egl1 libwebp7 libwebsocket-api-java
  libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1
  libxalan2-java libxau6 libxbean-reflect-java libxcb-dri2-0 libxcb-dri3-0
  libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0
  libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1
  libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1
  libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java
  libxml2 libxml2-utils libxmlgraphics-commons-java libxpp3-java libxrandr2
  libxrender1 libxshmfence1 libxss1 libxstream-java libxt6t64 libxtst6
  libxxf86vm1 libxz-java m4 man-db maven maven-debian-helper maven-repo-helper
  media-types ncbi-vdb-data netbase openjdk-21-jdk openjdk-21-jdk-headless
  openjdk-21-jre openjdk-21-jre-headless patchutils perl-openssl-defaults
  pkgconf pkgconf-bin po-debconf protobuf-compiler python3 python3-minimal
  python3.12 python3.12-minimal r-base-core r-cran-rjava sgml-base
  shared-mime-info testng ubuntu-mono ucf unzip velocity wdiff x11-common
  xdg-utils xkb-data zip zlib1g-dev
Suggested packages:
  ant-doc ivy libbcel-java libcommons-httpclient-java autoconf-archive
  gnu-standards autoconf-doc debtags dh-make adequate at autopkgtest
  bls-standalone bsd-mailx | mailx check-all-the-things cvs-buildpackage
  diffoscope disorderfs dose-extra duck elpa-devscripts faketime gnuplot
  how-can-i-help libauthen-sasl-perl libdbd-pg-perl libfile-desktopentry-perl
  libterm-size-perl libyaml-syck-perl mmdebstrap mutt piuparts
  postgresql-client pristine-lfs quilt ratt reprotest ssh-client
  svn-buildpackage w3m debian-keyring equivs libgitlab-api-v4-perl
  libsoap-lite-perl pristine-tar pinentry-gnome3 tor gettext-doc
  libasprintf-dev libgettextpo-dev parcimonie xloadimage gpg-wks-server groff
  alsa-utils libasound2-plugins libatinject-jsr330-api-java-doc colord
  libcommons-collections3-java-doc libcommons-collections4-java-doc
  libcommons-jxpath-java libcommons-vfs-java libcommons-lang-java-doc
  libavalon-framework-java libexcalibur-logkit-java cups-common libmsv-java
  libxpp2-java jython libjdom1-java low-memory-monitor libgoogle-gson-java-doc
  gvfs libcglib-java libdata-dump-perl picard-tools libio-compress-brotli-perl
  libxom-java libjboss-logging-java-doc libjcommander-java-doc jetty9
  libjoptsimple-java-doc libjsap-java-doc libjsoup-java-doc libjsr305-java-doc
  libjtidy-java-doc liblcms2-utils liblog4j1.2-java-doc libmail-java
  libcommons-csv-java libconversant-disruptor-java libdisruptor-java
  libgeronimo-jms-1.1-spec-java libjackson2-dataformat-xml-java
  libjackson2-dataformat-yaml libjctools-java libjeromq-java libwoodstox-java
  libjanino-java libtomcat9-java libcrypt-ssleay-perl
  libmaven-file-management-java-doc libmaven-shared-incremental-java-doc
  libmaven-shared-utils-java-doc libngs-java-doc libscalar-number-perl
  pciutils pcscd libeclipse-jdt-core-java libplexus-utils2-java-doc
  libplexus-velocity-java-doc libqdox-java-doc junit rhino lm-sensors
  libxstring-perl tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler
  gcj-jdk libsub-name-perl libbusiness-isbn-perl libregexp-ipv6-perl
  libauthen-ntlm-perl libxalan2-java-doc libbsf-java libxsltc-java
  libxerces2-java-doc libxml-commons-resolver1.1-java-doc
  libxmlgraphics-commons-java-doc libcglib-nodep-java libjdom2-java
  libjettison-java libjoda-time-java libkxml2-java m4-doc apparmor less
  www-browser apt-file licensecheck subversion openjdk-21-demo
  openjdk-21-source visualvm libnss-mdns fonts-dejavu-extra
  fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei
  | fonts-wqy-zenhei fonts-indic libmail-box-perl protobuf-mode-el python3-doc
  python3-tk python3-venv python3.12-venv python3.12-doc elpa-ess r-doc-info
  | r-doc-pdf r-mathlib r-base-html sgml-base-doc wdiff-doc
Recommended packages:
  librsvg2-common ant-optional dput | dupload libdistro-info-perl
  libgit-wrapper-perl libjson-perl liblist-compare-perl
  libstring-shellquote-perl licensecheck lintian python3-apt python3-debian
  python3-magic python3-requests python3-unidiff python3-xdg strace wget
  | curl curl | wget | lynx gnupg-l10n gpg-wks-client alsa-ucm-conf
  alsa-topology-conf at-spi2-core libdistlib-java-doc libarchive-cpio-perl
  icc-profiles-free libsaxon-java libgdk-pixbuf2.0-bin libgkl-jni
  libgl1-amber-dri libglib2.0-data xdg-user-dirs libgtk-3-bin
  libhtml-format-perl libldap-common libnamespace-clean-perl publicsuffix
  libsasl2-modules libltdl-dev mesa-vulkan-drivers | vulkan-icd
  libdata-dump-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl
  libxt-dev libatk-wrapper-java-jni fonts-dejavu-extra libmail-sendmail-perl
  r-recommended r-base-dev r-doc-html libyaml-snake-java libfile-mimeinfo-perl
  libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  adwaita-icon-theme ant ant-contrib at-spi2-common autoconf automake
  autopoint autotools-dev binfmt-support ca-certificates-java dbus dbus-bin
  dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session
  dconf-gsettings-backend dconf-service dctrl-tools debhelper debugedit
  default-jdk default-jdk-headless default-jre default-jre-headless devscripts
  dh-autoreconf dh-strip-nondeterminism dirmngr dwz fastjar file fontconfig
  fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base
  gnupg gnupg-utils gpgsm groff-base gtk-update-icon-cache hicolor-icon-theme
  humanity-icon-theme intltool-debian jarwrapper java-common java-wrappers
  javahelper junit4 junit5 keyboxd libactivation-java libaopalliance-java
  libapache-pom-java libapiguardian-java libarchive-zip-perl libasm-java
  libasound2-data libasound2t64 libatinject-jsr330-api-java
  libatk-bridge2.0-0t64 libatk1.0-0t64 libatspi2.0-0t64 libavahi-client3
  libavahi-common-data libavahi-common3 libb-hooks-op-check-perl
  libbarclay-java libbatik-java libblas3 libbrotli1 libbsd0 libbsh-java
  libbuild-helper-maven-plugin-java libbyte-buddy-java libcairo-gobject2
  libcairo2 libcdi-api-java libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libcolord2 libcolt-free-java
  libcommons-beanutils-java libcommons-cli-java libcommons-codec-java
  libcommons-collections3-java libcommons-collections4-java
  libcommons-compress-java libcommons-configuration-java
  libcommons-digester-java libcommons-exec-java libcommons-io-java
  libcommons-jexl2-java libcommons-lang-java libcommons-lang3-java
  libcommons-logging-java libcommons-math-java libcommons-math3-java
  libcommons-parent-java libcommons-text-java libcommons-validator-java
  libcups2t64 libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdebhelper-perl
  libdeflate0 libdevel-callchecker-perl libdistlib-java libdom4j-java
  libdoxia-core-java libdoxia-java libdoxia-sitetools-java libdrm-amdgpu1
  libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2
  libdsiutils-java libdw1t64 libdynaloader-functions-perl libeasymock-java
  libedit2 libel-api-java libelf1t64 libencode-locale-perl libepoxy0
  liberror-prone-java libexec-maven-plugin-java libexpat1 libfastutil-java
  libfile-dirlist-perl libfile-homedir-perl libfile-listing-perl
  libfile-stripnondeterminism-perl libfile-touch-perl libfile-which-perl
  libfontbox2-java libfontconfig1 libfop-java libfreemarker-java libfreetype6
  libfribidi0 libgatk-native-bindings-java libgdk-pixbuf-2.0-0
  libgdk-pixbuf2.0-common libgeronimo-annotation-1.3-spec-java
  libgeronimo-interceptor-3.0-spec-java libgfortran5 libgif7 libgkl-java
  libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0t64 libglvnd0 libglx-mesa0
  libglx0 libgoogle-gson-java libgraphite2-3 libgtk-3-0t64 libgtk-3-common
  libguava-java libguice-java libhamcrest-java libharfbuzz0b
  libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhtsjdk-java
  libhttp-cookies-perl libhttp-date-perl libhttp-message-perl
  libhttp-negotiate-perl libhttpclient-java libhttpcore-java libicb-utils-java
  libice6 libicu4j-java libicu74 libimport-into-perl libio-html-perl
  libio-pty-perl libio-socket-ssl-perl libipc-run-perl libitext1-java
  libjansi-java libjavassist-java libjaxb-api-java libjaxen-java
  libjaxp1.3-java libjbig0 libjboss-logging-java libjboss-vfs-java
  libjbzip2-java libjcommander-java libjetty9-java libjoptsimple-java
  libjpeg-turbo8 libjpeg8 libjsap-java libjsoup-java libjsp-api-java
  libjsr305-java libjtidy-java libksba8 liblapack3 liblcms2-2 libldap2
  liblerc4 liblightcouch-java libllvm17t64 liblog4j1.2-java liblog4j2-java
  liblogback-java liblwp-mediatypes-perl liblwp-protocol-https-perl
  libmagic-mgc libmagic1t64 libmaven-antrun-plugin-java libmaven-archiver-java
  libmaven-artifact-transfer-java libmaven-assembly-plugin-java
  libmaven-clean-plugin-java libmaven-common-artifact-filters-java
  libmaven-compiler-plugin-java libmaven-dependency-analyzer-java
  libmaven-dependency-plugin-java libmaven-dependency-tree-java
  libmaven-file-management-java libmaven-filtering-java libmaven-invoker-java
  libmaven-jar-plugin-java libmaven-javadoc-plugin-java libmaven-parent-java
  libmaven-plugin-tools-java libmaven-reporting-api-java
  libmaven-reporting-exec-java libmaven-reporting-impl-java
  libmaven-resolver-java libmaven-resources-plugin-java
  libmaven-shared-incremental-java libmaven-shared-io-java
  libmaven-shared-utils-java libmaven-site-plugin-java
  libmaven-source-plugin-java libmaven3-core-java libmbedcrypto7t64
  libmbedtls14t64 libmbedx509-1t64 libmjson-java libmodule-runtime-perl
  libmongodb-java libmoo-perl libncbi-ngs3 libncbi-vdb3 libnet-http-perl
  libnet-ssleay-perl libnghttp2-14 libngs-java libngs-jni libnspr4 libnss3
  libobjenesis-java libopentest4j-java libopentest4j-reporting-java
  liboro-java libpam-systemd libpango-1.0-0 libpangocairo-1.0-0
  libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl
  libpciaccess0 libpcsclite1 libpicard-java libpicocli-java libpipeline1
  libpixman-1-0 libpj-java libpkgconf3 libplexus-ant-factory-java
  libplexus-archiver-java libplexus-bsh-factory-java libplexus-build-api-java
  libplexus-cipher-java libplexus-classworlds-java libplexus-compiler-java
  libplexus-component-annotations-java libplexus-container-default-java
  libplexus-container-default1.5-java libplexus-i18n-java
  libplexus-interactivity-api-java libplexus-interpolation-java
  libplexus-io-java libplexus-languages-java libplexus-sec-dispatcher-java
  libplexus-utils2-java libplexus-velocity-java libprotobuf-dev
  libprotobuf-java libprotobuf-lite32t64 libprotobuf32t64 libprotoc32t64
  libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib
  libqdox-java libqdox2-java libreflections-java librhino-java
  librole-tiny-perl librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config
  libsensors5 libservlet-api-java libsharpyuv0 libsisu-inject-java
  libsisu-plexus-java libslf4j-java libsm6 libsnappy-java libsnappy-jni
  libsnappy1v5 libssh-4 libsub-override-perl libsub-quote-perl
  libsurefire-java libtcl8.6 libthai-data libthai0 libtiff6 libtimedate-perl
  libtk8.6 libtool libtry-tiny-perl libuchardet0 libunivocity-parsers-java
  liburi-perl libvelocity-tools-java libvulkan1 libwagon-file-java
  libwagon-http-shaded-java libwagon-provider-api-java libwayland-client0
  libwayland-cursor0 libwayland-egl1 libwebp7 libwebsocket-api-java
  libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1
  libxalan2-java libxau6 libxbean-reflect-java libxcb-dri2-0 libxcb-dri3-0
  libxcb-glx0 libxcb-present0 libxcb-randr0 libxcb-render0 libxcb-shm0
  libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1
  libxdmcp6 libxerces2-java libxext6 libxfixes3 libxft2 libxi6 libxinerama1
  libxkbcommon0 libxml-commons-external-java libxml-commons-resolver1.1-java
  libxml2 libxml2-utils libxmlgraphics-commons-java libxpp3-java libxrandr2
  libxrender1 libxshmfence1 libxss1 libxstream-java libxt6t64 libxtst6
  libxxf86vm1 libxz-java m4 man-db maven maven-debian-helper maven-repo-helper
  media-types ncbi-vdb-data netbase openjdk-21-jdk openjdk-21-jdk-headless
  openjdk-21-jre openjdk-21-jre-headless patchutils perl-openssl-defaults
  pkgconf pkgconf-bin po-debconf protobuf-compiler python3 python3-minimal
  python3.12 python3.12-minimal r-base-core r-cran-rjava
  sbuild-build-depends-main-dummy sgml-base shared-mime-info testng
  ubuntu-mono ucf unzip velocity wdiff x11-common xdg-utils xkb-data zip
  zlib1g-dev
0 upgraded, 440 newly installed, 0 to remove and 0 not upgraded.
Need to get 381 MB of archives.
After this operation, 934 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [938 B]
Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3.12-minimal amd64 3.12.3-1 [833 kB]
Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libexpat1 amd64 2.6.2-1 [86.9 kB]
Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 python3.12-minimal amd64 3.12.3-1 [2343 kB]
Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-minimal amd64 3.12.3-0ubuntu1 [27.2 kB]
Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 media-types all 10.1.0 [27.5 kB]
Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 netbase all 6.4 [13.1 kB]
Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [2067 kB]
Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 python3.12 amd64 3.12.3-1 [651 kB]
Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libpython3-stdlib amd64 3.12.3-0ubuntu1 [9890 B]
Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 python3 amd64 3.12.3-0ubuntu1 [24.1 kB]
Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libpipeline1 amd64 1.5.7-2 [23.6 kB]
Get:13 http://ftpmaster.internal/ubuntu oracular/universe amd64 binfmt-support amd64 2.2.2-7 [56.2 kB]
Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 sgml-base all 1.31 [11.4 kB]
Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libdbus-1-3 amd64 1.14.10-4ubuntu4 [210 kB]
Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 dbus-bin amd64 1.14.10-4ubuntu4 [39.3 kB]
Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 dbus-session-bus-common all 1.14.10-4ubuntu4 [80.4 kB]
Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 dbus-daemon amd64 1.14.10-4ubuntu4 [118 kB]
Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 dbus-system-bus-common all 1.14.10-4ubuntu4 [81.6 kB]
Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 dbus amd64 1.14.10-4ubuntu4 [24.3 kB]
Get:21 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-systemd amd64 256~rc1-1~exp2ubuntu1 [241 kB]
Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 dbus-user-session amd64 1.14.10-4ubuntu4 [9960 B]
Get:23 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libbsd0 amd64 0.12.2-1 [41.2 kB]
Get:24 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libelf1t64 amd64 0.191-1 [57.5 kB]
Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 libfribidi0 amd64 1.0.13-3build1 [26.1 kB]
Get:26 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libglib2.0-0t64 amd64 2.80.1-0ubuntu2 [1546 kB]
Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libicu74 amd64 74.2-1ubuntu3 [10.9 MB]
Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 libxml2 amd64 2.9.14+dfsg-1.3ubuntu3 [762 kB]
Get:29 http://ftpmaster.internal/ubuntu oracular/main amd64 shared-mime-info amd64 2.4-4 [474 kB]
Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 ucf all 3.0043+nmu1 [56.5 kB]
Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 xkb-data all 2.41-2ubuntu1 [395 kB]
Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 libmagic-mgc amd64 1:5.45-3build1 [307 kB]
Get:33 http://ftpmaster.internal/ubuntu oracular/main amd64 libmagic1t64 amd64 1:5.45-3build1 [87.2 kB]
Get:34 http://ftpmaster.internal/ubuntu oracular/main amd64 file amd64 1:5.45-3build1 [22.0 kB]
Get:35 http://ftpmaster.internal/ubuntu oracular/main amd64 gettext-base amd64 0.21-14ubuntu2 [38.4 kB]
Get:36 http://ftpmaster.internal/ubuntu oracular/main amd64 libuchardet0 amd64 0.0.8-1build1 [75.3 kB]
Get:37 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 groff-base amd64 1.23.0-4 [1020 kB]
Get:38 http://ftpmaster.internal/ubuntu oracular/main amd64 libdrm-common all 2.4.120-2build1 [8096 B]
Get:39 http://ftpmaster.internal/ubuntu oracular/main amd64 libdrm2 amd64 2.4.120-2build1 [40.5 kB]
Get:40 http://ftpmaster.internal/ubuntu oracular/main amd64 libedit2 amd64 3.1-20230828-1build1 [97.6 kB]
Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 libnghttp2-14 amd64 1.61.0-1 [74.8 kB]
Get:42 http://ftpmaster.internal/ubuntu oracular/main amd64 libpsl5t64 amd64 0.21.2-1.1build1 [57.1 kB]
Get:43 http://ftpmaster.internal/ubuntu oracular/main amd64 libsensors-config all 1:3.6.0-9build1 [5546 B]
Get:44 http://ftpmaster.internal/ubuntu oracular/main amd64 libsensors5 amd64 1:3.6.0-9build1 [26.6 kB]
Get:45 http://ftpmaster.internal/ubuntu oracular/main amd64 libxau6 amd64 1:1.0.9-1build6 [7160 B]
Get:46 http://ftpmaster.internal/ubuntu oracular/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu6 [10.3 kB]
Get:47 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb1 amd64 1.15-1ubuntu2 [47.7 kB]
Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 libx11-data all 2:1.8.7-1build1 [115 kB]
Get:49 http://ftpmaster.internal/ubuntu oracular/main amd64 libx11-6 amd64 2:1.8.7-1build1 [650 kB]
Get:50 http://ftpmaster.internal/ubuntu oracular/main amd64 libxext6 amd64 2:1.3.4-1build2 [30.4 kB]
Get:51 http://ftpmaster.internal/ubuntu oracular/main amd64 libxkbcommon0 amd64 1.6.0-1build1 [122 kB]
Get:52 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 man-db amd64 2.12.1-1 [1236 kB]
Get:53 http://ftpmaster.internal/ubuntu oracular/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3ubuntu3 [7852 B]
Get:54 http://ftpmaster.internal/ubuntu oracular/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu2 [150 kB]
Get:55 http://ftpmaster.internal/ubuntu oracular/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B]
Get:56 http://ftpmaster.internal/ubuntu oracular/main amd64 libdeflate0 amd64 1.20-1 [48.6 kB]
Get:57 http://ftpmaster.internal/ubuntu oracular/main amd64 libjbig0 amd64 2.1-6.1ubuntu2 [29.7 kB]
Get:58 http://ftpmaster.internal/ubuntu oracular/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu2 [179 kB]
Get:59 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [17.5 kB]
Get:60 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libwebp7 amd64 1.4.0-0.1 [231 kB]
Get:61 http://ftpmaster.internal/ubuntu oracular/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu2 [199 kB]
Get:62 http://ftpmaster.internal/ubuntu oracular/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3ubuntu3 [147 kB]
Get:63 http://ftpmaster.internal/ubuntu oracular/main amd64 gtk-update-icon-cache amd64 3.24.41-4ubuntu1 [51.6 kB]
Get:64 http://ftpmaster.internal/ubuntu oracular/main amd64 hicolor-icon-theme all 0.17-2 [9976 B]
Get:65 http://ftpmaster.internal/ubuntu oracular/main amd64 humanity-icon-theme all 0.6.16 [1282 kB]
Get:66 http://ftpmaster.internal/ubuntu oracular/main amd64 ubuntu-mono all 24.04-0ubuntu1 [151 kB]
Get:67 http://ftpmaster.internal/ubuntu oracular/main amd64 adwaita-icon-theme all 46.0-1 [723 kB]
Get:68 http://ftpmaster.internal/ubuntu oracular/main amd64 ca-certificates-java all 20240118 [11.6 kB]
Get:69 http://ftpmaster.internal/ubuntu oracular/main amd64 java-common all 0.75+exp1 [6798 B]
Get:70 http://ftpmaster.internal/ubuntu oracular/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB]
Get:71 http://ftpmaster.internal/ubuntu oracular/main amd64 libnspr4 amd64 2:4.35-1.1build1 [117 kB]
Get:72 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libnss3 amd64 2:3.99-1 [1472 kB]
Get:73 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpcsclite1 amd64 2.2.1-1 [23.5 kB]
Get:74 http://ftpmaster.internal/ubuntu oracular/main amd64 openjdk-21-jre-headless amd64 21.0.3+9-1ubuntu1 [46.6 MB]
Get:75 http://ftpmaster.internal/ubuntu oracular/main amd64 default-jre-headless amd64 2:1.21-75+exp1 [3094 B]
Get:76 http://ftpmaster.internal/ubuntu oracular/universe amd64 ant all 1.10.14-1 [2147 kB]
Get:77 http://ftpmaster.internal/ubuntu oracular/main amd64 at-spi2-common all 2.52.0-1build1 [8674 B]
Get:78 http://ftpmaster.internal/ubuntu oracular/main amd64 m4 amd64 1.4.19-4build1 [244 kB]
Get:79 http://ftpmaster.internal/ubuntu oracular/main amd64 autoconf all 2.71-3 [339 kB]
Get:80 http://ftpmaster.internal/ubuntu oracular/main amd64 autotools-dev all 20220109.1 [44.9 kB]
Get:81 http://ftpmaster.internal/ubuntu oracular/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB]
Get:82 http://ftpmaster.internal/ubuntu oracular/main amd64 autopoint all 0.21-14ubuntu2 [422 kB]
Get:83 http://ftpmaster.internal/ubuntu oracular/main amd64 libdconf1 amd64 0.40.0-4build2 [39.4 kB]
Get:84 http://ftpmaster.internal/ubuntu oracular/main amd64 dconf-service amd64 0.40.0-4build2 [27.5 kB]
Get:85 http://ftpmaster.internal/ubuntu oracular/main amd64 dconf-gsettings-backend amd64 0.40.0-4build2 [22.1 kB]
Get:86 http://ftpmaster.internal/ubuntu oracular/main amd64 dctrl-tools amd64 2.24-3build3 [106 kB]
Get:87 http://ftpmaster.internal/ubuntu oracular/main amd64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB]
Get:88 http://ftpmaster.internal/ubuntu oracular/main amd64 libtool all 2.4.7-7build1 [166 kB]
Get:89 http://ftpmaster.internal/ubuntu oracular/main amd64 dh-autoreconf all 20 [16.1 kB]
Get:90 http://ftpmaster.internal/ubuntu oracular/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB]
Get:91 http://ftpmaster.internal/ubuntu oracular/main amd64 libsub-override-perl all 0.10-1 [10.0 kB]
Get:92 http://ftpmaster.internal/ubuntu oracular/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB]
Get:93 http://ftpmaster.internal/ubuntu oracular/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B]
Get:94 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libdw1t64 amd64 0.191-1 [265 kB]
Get:95 http://ftpmaster.internal/ubuntu oracular/main amd64 debugedit amd64 1:5.0-5build2 [46.1 kB]
Get:96 http://ftpmaster.internal/ubuntu oracular/main amd64 dwz amd64 0.15-1build6 [115 kB]
Get:97 http://ftpmaster.internal/ubuntu oracular/main amd64 gettext amd64 0.21-14ubuntu2 [864 kB]
Get:98 http://ftpmaster.internal/ubuntu oracular/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB]
Get:99 http://ftpmaster.internal/ubuntu oracular/main amd64 po-debconf all 1.0.21+nmu1 [233 kB]
Get:100 http://ftpmaster.internal/ubuntu oracular/main amd64 debhelper all 13.14.1ubuntu5 [869 kB]
Get:101 http://ftpmaster.internal/ubuntu oracular/main amd64 libatk1.0-0t64 amd64 2.52.0-1build1 [55.3 kB]
Get:102 http://ftpmaster.internal/ubuntu oracular/main amd64 libxi6 amd64 2:1.8.1-1build1 [32.4 kB]
Get:103 http://ftpmaster.internal/ubuntu oracular/main amd64 libatspi2.0-0t64 amd64 2.52.0-1build1 [80.5 kB]
Get:104 http://ftpmaster.internal/ubuntu oracular/main amd64 libatk-bridge2.0-0t64 amd64 2.52.0-1build1 [66.0 kB]
Get:105 http://ftpmaster.internal/ubuntu oracular/main amd64 libbrotli1 amd64 1.1.0-2build2 [331 kB]
Get:106 http://ftpmaster.internal/ubuntu oracular/main amd64 libfreetype6 amd64 2.13.2+dfsg-1build3 [402 kB]
Get:107 http://ftpmaster.internal/ubuntu oracular/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB]
Get:108 http://ftpmaster.internal/ubuntu oracular/main amd64 fonts-dejavu-core all 2.37-8 [835 kB]
Get:109 http://ftpmaster.internal/ubuntu oracular/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB]
Get:110 http://ftpmaster.internal/ubuntu oracular/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB]
Get:111 http://ftpmaster.internal/ubuntu oracular/main amd64 libpixman-1-0 amd64 0.42.2-1build1 [279 kB]
Get:112 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-render0 amd64 1.15-1ubuntu2 [16.2 kB]
Get:113 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-shm0 amd64 1.15-1ubuntu2 [5756 B]
Get:114 http://ftpmaster.internal/ubuntu oracular/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB]
Get:115 http://ftpmaster.internal/ubuntu oracular/main amd64 libcairo2 amd64 1.18.0-3build1 [566 kB]
Get:116 http://ftpmaster.internal/ubuntu oracular/main amd64 libcairo-gobject2 amd64 1.18.0-3build1 [127 kB]
Get:117 http://ftpmaster.internal/ubuntu oracular/main amd64 libcolord2 amd64 1.4.7-1build2 [149 kB]
Get:118 http://ftpmaster.internal/ubuntu oracular/main amd64 libavahi-common-data amd64 0.8-13ubuntu6 [29.7 kB]
Get:119 http://ftpmaster.internal/ubuntu oracular/main amd64 libavahi-common3 amd64 0.8-13ubuntu6 [23.3 kB]
Get:120 http://ftpmaster.internal/ubuntu oracular/main amd64 libavahi-client3 amd64 0.8-13ubuntu6 [26.8 kB]
Get:121 http://ftpmaster.internal/ubuntu oracular/main amd64 libcups2t64 amd64 2.4.7-1.2ubuntu7 [270 kB]
Get:122 http://ftpmaster.internal/ubuntu oracular/main amd64 libepoxy0 amd64 1.5.10-1build1 [220 kB]
Get:123 http://ftpmaster.internal/ubuntu oracular/main amd64 libgraphite2-3 amd64 1.3.14-2build1 [73.0 kB]
Get:124 http://ftpmaster.internal/ubuntu oracular/main amd64 libharfbuzz0b amd64 8.3.0-2build2 [469 kB]
Get:125 http://ftpmaster.internal/ubuntu oracular/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB]
Get:126 http://ftpmaster.internal/ubuntu oracular/main amd64 libthai-data all 0.1.29-2build1 [158 kB]
Get:127 http://ftpmaster.internal/ubuntu oracular/main amd64 libdatrie1 amd64 0.2.13-3build1 [19.0 kB]
Get:128 http://ftpmaster.internal/ubuntu oracular/main amd64 libthai0 amd64 0.1.29-2build1 [18.9 kB]
Get:129 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpango-1.0-0 amd64 1.52.2+ds-1 [233 kB]
Get:130 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpangoft2-1.0-0 amd64 1.52.2+ds-1 [42.6 kB]
Get:131 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpangocairo-1.0-0 amd64 1.52.2+ds-1 [28.7 kB]
Get:132 http://ftpmaster.internal/ubuntu oracular/main amd64 libwayland-client0 amd64 1.22.0-2.1build1 [26.4 kB]
Get:133 http://ftpmaster.internal/ubuntu oracular/main amd64 libwayland-cursor0 amd64 1.22.0-2.1build1 [10.4 kB]
Get:134 http://ftpmaster.internal/ubuntu oracular/main amd64 libwayland-egl1 amd64 1.22.0-2.1build1 [5628 B]
Get:135 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcomposite1 amd64 1:0.4.5-1build3 [6320 B]
Get:136 http://ftpmaster.internal/ubuntu oracular/main amd64 libxfixes3 amd64 1:6.0.0-2build1 [10.8 kB]
Get:137 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcursor1 amd64 1:1.2.1-1build1 [20.7 kB]
Get:138 http://ftpmaster.internal/ubuntu oracular/main amd64 libxdamage1 amd64 1:1.1.6-1build1 [6150 B]
Get:139 http://ftpmaster.internal/ubuntu oracular/main amd64 libxinerama1 amd64 2:1.1.4-3build1 [6396 B]
Get:140 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libxrandr2 amd64 2:1.5.4-1 [19.6 kB]
Get:141 http://ftpmaster.internal/ubuntu oracular/main amd64 libgtk-3-common all 3.24.41-4ubuntu1 [1202 kB]
Get:142 http://ftpmaster.internal/ubuntu oracular/main amd64 libgtk-3-0t64 amd64 3.24.41-4ubuntu1 [2901 kB]
Get:143 http://ftpmaster.internal/ubuntu oracular/main amd64 libglvnd0 amd64 1.7.0-1build1 [69.6 kB]
Get:144 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libglapi-mesa amd64 24.0.7-1ubuntu1 [42.5 kB]
Get:145 http://ftpmaster.internal/ubuntu oracular/main amd64 libx11-xcb1 amd64 2:1.8.7-1build1 [7800 B]
Get:146 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-dri2-0 amd64 1.15-1ubuntu2 [7222 B]
Get:147 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-dri3-0 amd64 1.15-1ubuntu2 [7142 B]
Get:148 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-glx0 amd64 1.15-1ubuntu2 [24.8 kB]
Get:149 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-present0 amd64 1.15-1ubuntu2 [5676 B]
Get:150 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-randr0 amd64 1.15-1ubuntu2 [17.9 kB]
Get:151 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-sync1 amd64 1.15-1ubuntu2 [9312 B]
Get:152 http://ftpmaster.internal/ubuntu oracular/main amd64 libxcb-xfixes0 amd64 1.15-1ubuntu2 [10.2 kB]
Get:153 http://ftpmaster.internal/ubuntu oracular/main amd64 libxshmfence1 amd64 1.3-1build5 [4764 B]
Get:154 http://ftpmaster.internal/ubuntu oracular/main amd64 libxxf86vm1 amd64 1:1.1.4-1build4 [9282 B]
Get:155 http://ftpmaster.internal/ubuntu oracular/main amd64 libvulkan1 amd64 1.3.280.0-1 [141 kB]
Get:156 http://ftpmaster.internal/ubuntu oracular/main amd64 libdrm-amdgpu1 amd64 2.4.120-2build1 [20.2 kB]
Get:157 http://ftpmaster.internal/ubuntu oracular/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB]
Get:158 http://ftpmaster.internal/ubuntu oracular/main amd64 libdrm-intel1 amd64 2.4.120-2build1 [63.8 kB]
Get:159 http://ftpmaster.internal/ubuntu oracular/main amd64 libdrm-nouveau2 amd64 2.4.120-2build1 [17.7 kB]
Get:160 http://ftpmaster.internal/ubuntu oracular/main amd64 libdrm-radeon1 amd64 2.4.120-2build1 [20.8 kB]
Get:161 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libllvm17t64 amd64 1:17.0.6-12 [26.2 MB]
Get:162 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgl1-mesa-dri amd64 24.0.7-1ubuntu1 [8942 kB]
Get:163 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libglx-mesa0 amd64 24.0.7-1ubuntu1 [154 kB]
Get:164 http://ftpmaster.internal/ubuntu oracular/main amd64 libglx0 amd64 1.7.0-1build1 [38.6 kB]
Get:165 http://ftpmaster.internal/ubuntu oracular/main amd64 libgl1 amd64 1.7.0-1build1 [102 kB]
Get:166 http://ftpmaster.internal/ubuntu oracular/main amd64 libasound2-data all 1.2.11-1build2 [21.0 kB]
Get:167 http://ftpmaster.internal/ubuntu oracular/main amd64 libasound2t64 amd64 1.2.11-1build2 [399 kB]
Get:168 http://ftpmaster.internal/ubuntu oracular/main amd64 libgif7 amd64 5.2.2-1ubuntu1 [35.2 kB]
Get:169 http://ftpmaster.internal/ubuntu oracular/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB]
Get:170 http://ftpmaster.internal/ubuntu oracular/main amd64 libxtst6 amd64 2:1.2.3-1.1build1 [12.6 kB]
Get:171 http://ftpmaster.internal/ubuntu oracular/main amd64 openjdk-21-jre amd64 21.0.3+9-1ubuntu1 [226 kB]
Get:172 http://ftpmaster.internal/ubuntu oracular/main amd64 default-jre amd64 2:1.21-75+exp1 [922 B]
Get:173 http://ftpmaster.internal/ubuntu oracular/main amd64 openjdk-21-jdk-headless amd64 21.0.3+9-1ubuntu1 [82.5 MB]
Get:174 http://ftpmaster.internal/ubuntu oracular/main amd64 default-jdk-headless amd64 2:1.21-75+exp1 [960 B]
Get:175 http://ftpmaster.internal/ubuntu oracular/main amd64 openjdk-21-jdk amd64 21.0.3+9-1ubuntu1 [3699 kB]
Get:176 http://ftpmaster.internal/ubuntu oracular/main amd64 default-jdk amd64 2:1.21-75+exp1 [926 B]
Get:177 http://ftpmaster.internal/ubuntu oracular/main amd64 libksba8 amd64 1.6.6-1build1 [122 kB]
Get:178 http://ftpmaster.internal/ubuntu oracular/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-5ubuntu3 [20.3 kB]
Get:179 http://ftpmaster.internal/ubuntu oracular/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-5ubuntu3 [53.2 kB]
Get:180 http://ftpmaster.internal/ubuntu oracular/main amd64 libldap2 amd64 2.6.7+dfsg-1~exp1ubuntu8 [195 kB]
Get:181 http://ftpmaster.internal/ubuntu oracular/main amd64 dirmngr amd64 2.4.4-2ubuntu17 [323 kB]
Get:182 http://ftpmaster.internal/ubuntu oracular/main amd64 gnupg-utils amd64 2.4.4-2ubuntu17 [108 kB]
Get:183 http://ftpmaster.internal/ubuntu oracular/main amd64 gpgsm amd64 2.4.4-2ubuntu17 [232 kB]
Get:184 http://ftpmaster.internal/ubuntu oracular/main amd64 keyboxd amd64 2.4.4-2ubuntu17 [78.3 kB]
Get:185 http://ftpmaster.internal/ubuntu oracular/main amd64 gnupg all 2.4.4-2ubuntu17 [359 kB]
Get:186 http://ftpmaster.internal/ubuntu oracular/main amd64 libfile-dirlist-perl all 0.05-3 [7286 B]
Get:187 http://ftpmaster.internal/ubuntu oracular/main amd64 libfile-which-perl all 1.27-2 [12.5 kB]
Get:188 http://ftpmaster.internal/ubuntu oracular/main amd64 libfile-homedir-perl all 1.006-2 [37.0 kB]
Get:189 http://ftpmaster.internal/ubuntu oracular/main amd64 libfile-touch-perl all 0.12-2 [7498 B]
Get:190 http://ftpmaster.internal/ubuntu oracular/main amd64 libio-pty-perl amd64 1:1.20-1build2 [31.2 kB]
Get:191 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libipc-run-perl all 20231003.0-2 [91.5 kB]
Get:192 http://ftpmaster.internal/ubuntu oracular/main amd64 libclass-method-modifiers-perl all 2.15-1 [16.1 kB]
Get:193 http://ftpmaster.internal/ubuntu oracular/main amd64 libclass-xsaccessor-perl amd64 1.19-4build4 [33.1 kB]
Get:194 http://ftpmaster.internal/ubuntu oracular/main amd64 libb-hooks-op-check-perl amd64 0.22-3build1 [9518 B]
Get:195 http://ftpmaster.internal/ubuntu oracular/main amd64 libdynaloader-functions-perl all 0.003-3 [12.1 kB]
Get:196 http://ftpmaster.internal/ubuntu oracular/main amd64 libdevel-callchecker-perl amd64 0.009-1 [14.4 kB]
Get:197 http://ftpmaster.internal/ubuntu oracular/main amd64 libparams-classify-perl amd64 0.015-2build5 [20.1 kB]
Get:198 http://ftpmaster.internal/ubuntu oracular/main amd64 libmodule-runtime-perl all 0.016-2 [16.4 kB]
Get:199 http://ftpmaster.internal/ubuntu oracular/main amd64 libimport-into-perl all 1.002005-2 [10.7 kB]
Get:200 http://ftpmaster.internal/ubuntu oracular/main amd64 librole-tiny-perl all 2.002004-1 [16.3 kB]
Get:201 http://ftpmaster.internal/ubuntu oracular/main amd64 libsub-quote-perl all 2.006008-1ubuntu1 [20.7 kB]
Get:202 http://ftpmaster.internal/ubuntu oracular/main amd64 libmoo-perl all 2.005005-1 [47.4 kB]
Get:203 http://ftpmaster.internal/ubuntu oracular/main amd64 libencode-locale-perl all 1.05-3 [11.6 kB]
Get:204 http://ftpmaster.internal/ubuntu oracular/main amd64 libtimedate-perl all 2.3300-2 [34.0 kB]
Get:205 http://ftpmaster.internal/ubuntu oracular/main amd64 libhttp-date-perl all 6.06-1 [10.2 kB]
Get:206 http://ftpmaster.internal/ubuntu oracular/main amd64 libfile-listing-perl all 6.16-1 [11.3 kB]
Get:207 http://ftpmaster.internal/ubuntu oracular/main amd64 libhtml-tagset-perl all 3.24-1 [14.1 kB]
Get:208 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 liburi-perl all 5.28-1 [88.1 kB]
Get:209 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libhtml-parser-perl amd64 3.82-1 [85.6 kB]
Get:210 http://ftpmaster.internal/ubuntu oracular/main amd64 libhtml-tree-perl all 5.07-3 [200 kB]
Get:211 http://ftpmaster.internal/ubuntu oracular/main amd64 libclone-perl amd64 0.46-1build3 [10.7 kB]
Get:212 http://ftpmaster.internal/ubuntu oracular/main amd64 libio-html-perl all 1.004-3 [15.9 kB]
Get:213 http://ftpmaster.internal/ubuntu oracular/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.1 kB]
Get:214 http://ftpmaster.internal/ubuntu oracular/main amd64 libhttp-message-perl all 6.45-1ubuntu1 [78.2 kB]
Get:215 http://ftpmaster.internal/ubuntu oracular/main amd64 libhttp-cookies-perl all 6.11-1 [18.2 kB]
Get:216 http://ftpmaster.internal/ubuntu oracular/main amd64 libhttp-negotiate-perl all 6.01-2 [12.4 kB]
Get:217 http://ftpmaster.internal/ubuntu oracular/main amd64 perl-openssl-defaults amd64 7build3 [6626 B]
Get:218 http://ftpmaster.internal/ubuntu oracular/main amd64 libnet-ssleay-perl amd64 1.94-1build4 [316 kB]
Get:219 http://ftpmaster.internal/ubuntu oracular/main amd64 libio-socket-ssl-perl all 2.085-1 [195 kB]
Get:220 http://ftpmaster.internal/ubuntu oracular/main amd64 libnet-http-perl all 6.23-1 [22.3 kB]
Get:221 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 liblwp-protocol-https-perl all 6.14-1 [9040 B]
Get:222 http://ftpmaster.internal/ubuntu oracular/main amd64 libtry-tiny-perl all 0.31-2 [20.8 kB]
Get:223 http://ftpmaster.internal/ubuntu oracular/main amd64 libwww-robotrules-perl all 6.02-1 [12.6 kB]
Get:224 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libwww-perl all 6.77-1 [138 kB]
Get:225 http://ftpmaster.internal/ubuntu oracular/main amd64 patchutils amd64 0.4.2-1build3 [77.0 kB]
Get:226 http://ftpmaster.internal/ubuntu oracular/main amd64 wdiff amd64 1.2.2-6build1 [29.1 kB]
Get:227 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 devscripts all 2.23.7ubuntu1 [1048 kB]
Get:228 http://ftpmaster.internal/ubuntu oracular/universe amd64 fastjar amd64 2:0.98-7 [67.1 kB]
Get:229 http://ftpmaster.internal/ubuntu oracular/universe amd64 jarwrapper all 0.79 [10.3 kB]
Get:230 http://ftpmaster.internal/ubuntu oracular/main amd64 unzip amd64 6.0-28ubuntu4 [175 kB]
Get:231 http://ftpmaster.internal/ubuntu oracular/universe amd64 java-wrappers all 0.4 [8662 B]
Get:232 http://ftpmaster.internal/ubuntu oracular/universe amd64 javahelper all 0.79 [83.5 kB]
Get:233 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhamcrest-java all 2.2-2 [117 kB]
Get:234 http://ftpmaster.internal/ubuntu oracular/universe amd64 junit4 all 4.13.2-4 [347 kB]
Get:235 http://ftpmaster.internal/ubuntu oracular/universe amd64 libapiguardian-java all 1.1.2-1 [4598 B]
Get:236 http://ftpmaster.internal/ubuntu oracular/universe amd64 libopentest4j-java all 1.2.0-4 [9396 B]
Get:237 http://ftpmaster.internal/ubuntu oracular/universe amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.3 kB]
Get:238 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpicocli-java all 4.6.2-2 [387 kB]
Get:239 http://ftpmaster.internal/ubuntu oracular/universe amd64 libunivocity-parsers-java all 2.9.1-1 [394 kB]
Get:240 http://ftpmaster.internal/ubuntu oracular/universe amd64 junit5 all 5.10.1-1 [2446 kB]
Get:241 http://ftpmaster.internal/ubuntu oracular/universe amd64 libactivation-java all 1.2.0-2 [84.7 kB]
Get:242 http://ftpmaster.internal/ubuntu oracular/universe amd64 libapache-pom-java all 29-2 [5284 B]
Get:243 http://ftpmaster.internal/ubuntu oracular/universe amd64 libasm-java all 9.7-1 [392 kB]
Get:244 http://ftpmaster.internal/ubuntu oracular/universe amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5348 B]
Get:245 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-parent-java all 56-1 [10.7 kB]
Get:246 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-lang3-java all 3.14.0-1 [586 kB]
Get:247 http://ftpmaster.internal/ubuntu oracular/universe amd64 libfreemarker-java all 2.3.32-2 [1542 kB]
Get:248 http://ftpmaster.internal/ubuntu oracular/universe amd64 libgoogle-gson-java all 2.10.1-1 [252 kB]
Get:249 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB]
Get:250 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-codec-java all 1.16.0-1 [306 kB]
Get:251 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-logging-java all 1.3.0-1ubuntu1 [63.8 kB]
Get:252 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhttpcore-java all 4.4.16-1 [612 kB]
Get:253 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhttpclient-java all 4.5.14-1 [1241 kB]
Get:254 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblightcouch-java all 0.2.0-1 [74.2 kB]
Get:255 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmongodb-java all 3.6.3-2 [1899 kB]
Get:256 http://ftpmaster.internal/ubuntu oracular/universe amd64 libslf4j-java all 1.7.32-1 [141 kB]
Get:257 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblog4j2-java all 2.19.0-2 [2294 kB]
Get:258 http://ftpmaster.internal/ubuntu oracular/universe amd64 libbarclay-java all 5.0.0+dfsg-1 [108 kB]
Get:259 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjaxp1.3-java all 1.3.05-6 [227 kB]
Get:260 http://ftpmaster.internal/ubuntu oracular/universe amd64 libxml-commons-external-java all 1.4.01-6 [240 kB]
Get:261 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 libcommons-io-java all 2.16.1-1 [451 kB]
Get:262 http://ftpmaster.internal/ubuntu oracular/universe amd64 libxmlgraphics-commons-java all 2.8-2 [619 kB]
Get:263 http://ftpmaster.internal/ubuntu oracular/universe amd64 libbatik-java all 1.17+dfsg-1 [3877 kB]
Get:264 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB]
Get:265 http://ftpmaster.internal/ubuntu oracular/universe amd64 libbsh-java all 2.0b4-20 [289 kB]
Get:266 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-shared-utils-java all 3.3.4-1 [137 kB]
Get:267 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-cli-java all 1.6.0-1 [59.9 kB]
Get:268 http://ftpmaster.internal/ubuntu oracular/universe amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.2 kB]
Get:269 http://ftpmaster.internal/ubuntu oracular/universe amd64 libaopalliance-java all 20070526-7 [8166 B]
Get:270 http://ftpmaster.internal/ubuntu oracular/universe amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get:271 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjsr305-java all 0.1~+svn49-11 [27.0 kB]
Get:272 http://ftpmaster.internal/ubuntu oracular/universe amd64 libguava-java all 32.0.1-1 [2692 kB]
Get:273 http://ftpmaster.internal/ubuntu oracular/universe amd64 libguice-java all 4.2.3-2 [1434 kB]
Get:274 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-parent-java all 35-1 [5810 B]
Get:275 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-utils2-java all 3.4.2-1 [256 kB]
Get:276 http://ftpmaster.internal/ubuntu oracular/universe amd64 libwagon-provider-api-java all 3.5.3-1 [47.9 kB]
Get:277 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-resolver-java all 1.6.3-1 [544 kB]
Get:278 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-cipher-java all 2.0-1 [14.7 kB]
Get:279 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-classworlds-java all 2.7.0-1 [50.0 kB]
Get:280 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-component-annotations-java all 2.1.1-1 [6550 B]
Get:281 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB]
Get:282 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.1 kB]
Get:283 http://ftpmaster.internal/ubuntu oracular/universe amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4fakesync [8616 B]
Get:284 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcdi-api-java all 1.2-3 [54.3 kB]
Get:285 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsisu-inject-java all 0.3.4-2 [347 kB]
Get:286 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsisu-plexus-java all 0.3.4-3 [181 kB]
Get:287 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven3-core-java all 3.8.7-2 [1565 kB]
Get:288 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-shared-io-java all 3.0.0-4 [32.6 kB]
Get:289 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB]
Get:290 http://ftpmaster.internal/ubuntu oracular/universe amd64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB]
Get:291 http://ftpmaster.internal/ubuntu oracular/universe amd64 libbyte-buddy-java all 1.14.13-1 [4706 kB]
Get:292 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcolt-free-java all 1.2.0+dfsg-8 [438 kB]
Get:293 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-collections3-java all 3.2.2-3 [526 kB]
Get:294 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-beanutils-java all 1.9.4-2 [228 kB]
Get:295 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-collections4-java all 4.4-2 [670 kB]
Get:296 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-compress-java all 1.25.0-1 [612 kB]
Get:297 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-lang-java all 2.6-10 [270 kB]
Get:298 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-configuration-java all 1.10-6 [342 kB]
Get:299 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-digester-java all 1.8.1-6 [136 kB]
Get:300 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-exec-java all 1.3-2 [48.1 kB]
Get:301 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-jexl2-java all 2.1.1-6 [250 kB]
Get:302 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-math-java all 2.2-8 [921 kB]
Get:303 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-math3-java all 3.6.1-3 [2016 kB]
Get:304 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-io-java all 3.3.1-2 [64.4 kB]
Get:305 http://ftpmaster.internal/ubuntu oracular/main amd64 libsnappy1v5 amd64 1.2.0-2 [30.3 kB]
Get:306 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsnappy-jni amd64 1.1.10.5-2 [6622 B]
Get:307 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsnappy-java all 1.1.10.5-2 [83.7 kB]
Get:308 http://ftpmaster.internal/ubuntu oracular/universe amd64 libxz-java all 1.9-1 [140 kB]
Get:309 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-archiver-java all 4.6.1-1 [185 kB]
Get:310 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-archiver-java all 3.6.0-1 [25.3 kB]
Get:311 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-jar-plugin-java all 3.3.0-2 [23.9 kB]
Get:312 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-text-java all 1.11.0-1 [215 kB]
Get:313 http://ftpmaster.internal/ubuntu oracular/universe amd64 libcommons-validator-java all 1:1.7-1 [178 kB]
Get:314 http://ftpmaster.internal/ubuntu oracular/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build7 [56.3 kB]
Get:315 http://ftpmaster.internal/ubuntu oracular/main amd64 libssh-4 amd64 0.10.6-2build2 [188 kB]
Get:316 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libcurl4t64 amd64 8.5.0-2ubuntu10.1 [341 kB]
Get:317 http://ftpmaster.internal/ubuntu oracular/universe amd64 libdistlib-java all 1.0-4 [72.0 kB]
Get:318 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjaxen-java all 1.1.6-4 [214 kB]
Get:319 http://ftpmaster.internal/ubuntu oracular/universe amd64 libdom4j-java all 2.1.4-1 [310 kB]
Get:320 http://ftpmaster.internal/ubuntu oracular/universe amd64 libdoxia-core-java all 1.12.0-1 [212 kB]
Get:321 http://ftpmaster.internal/ubuntu oracular/universe amd64 libfontbox2-java all 2.0.29-1 [1507 kB]
Get:322 http://ftpmaster.internal/ubuntu oracular/universe amd64 libqdox-java all 1.12.1-3 [172 kB]
Get:323 http://ftpmaster.internal/ubuntu oracular/universe amd64 libfop-java all 1:2.8-3 [10.3 MB]
Get:324 http://ftpmaster.internal/ubuntu oracular/universe amd64 libitext1-java all 1.4-7 [1257 kB]
Get:325 http://ftpmaster.internal/ubuntu oracular/universe amd64 libxbean-reflect-java all 4.5-8 [132 kB]
Get:326 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-container-default-java all 2.1.1-1 [191 kB]
Get:327 http://ftpmaster.internal/ubuntu oracular/universe amd64 libdoxia-java all 1.12.0-1 [458 kB]
Get:328 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-reporting-api-java all 3.1.1-1 [7172 B]
Get:329 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-i18n-java all 1.0-beta-10-6 [12.9 kB]
Get:330 http://ftpmaster.internal/ubuntu oracular/universe amd64 velocity all 1.7-7 [432 kB]
Get:331 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-velocity-java all 1.2-3.1 [10.5 kB]
Get:332 http://ftpmaster.internal/ubuntu oracular/universe amd64 liboro-java all 2.0.8a-14 [65.0 kB]
Get:333 http://ftpmaster.internal/ubuntu oracular/universe amd64 libvelocity-tools-java all 2.0-9 [309 kB]
Get:334 http://ftpmaster.internal/ubuntu oracular/universe amd64 libxml-commons-resolver1.1-java all 1.2-11 [97.6 kB]
Get:335 http://ftpmaster.internal/ubuntu oracular/universe amd64 libxerces2-java all 2.12.2-1 [1430 kB]
Get:336 http://ftpmaster.internal/ubuntu oracular/universe amd64 libxalan2-java all 2.7.2-4 [3416 kB]
Get:337 http://ftpmaster.internal/ubuntu oracular/universe amd64 libdoxia-sitetools-java all 1.11.1-1 [202 kB]
Get:338 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 libfastutil-java all 8.5.12+dfsg-2 [20.0 MB]
Get:339 http://ftpmaster.internal/ubuntu oracular/universe amd64 libxpp3-java all 1.1.4c-3 [292 kB]
Get:340 http://ftpmaster.internal/ubuntu oracular/universe amd64 libxstream-java all 1.4.20-1 [561 kB]
Get:341 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjsap-java all 2.1-5 [100 kB]
Get:342 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblogback-java all 1:1.2.11-5 [697 kB]
Get:343 http://ftpmaster.internal/ubuntu oracular/universe amd64 libdsiutils-java all 2.7.3+dfsg-1 [511 kB]
Get:344 http://ftpmaster.internal/ubuntu oracular/universe amd64 libobjenesis-java all 3.3-3 [41.1 kB]
Get:345 http://ftpmaster.internal/ubuntu oracular/universe amd64 libeasymock-java all 5.2.0-1 [128 kB]
Get:346 http://ftpmaster.internal/ubuntu oracular/universe amd64 libel-api-java all 3.0.0-3 [64.9 kB]
Get:347 http://ftpmaster.internal/ubuntu oracular/universe amd64 libexec-maven-plugin-java all 3.1.0-2 [66.1 kB]
Get:348 http://ftpmaster.internal/ubuntu oracular/universe amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8014 B]
Get:349 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgfortran5 amd64 14-20240429-1ubuntu1 [928 kB]
Get:350 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmjson-java all 1.4.0-3 [60.4 kB]
Get:351 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmbedcrypto7t64 amd64 2.28.8-1 [209 kB]
Get:352 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmbedx509-1t64 amd64 2.28.8-1 [46.6 kB]
Get:353 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmbedtls14t64 amd64 2.28.8-1 [82.2 kB]
Get:354 http://ftpmaster.internal/ubuntu oracular/universe amd64 ncbi-vdb-data all 3.0.2+dfsg-2build2 [67.5 kB]
Get:355 http://ftpmaster.internal/ubuntu oracular/universe amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2build2 [1112 kB]
Get:356 http://ftpmaster.internal/ubuntu oracular/universe amd64 libncbi-ngs3 amd64 3.0.3+dfsg-6ubuntu5 [153 kB]
Get:357 http://ftpmaster.internal/ubuntu oracular/universe amd64 libngs-jni amd64 3.0.3+dfsg-6ubuntu5 [4836 B]
Get:358 http://ftpmaster.internal/ubuntu oracular/universe amd64 libngs-java amd64 3.0.3+dfsg-6ubuntu5 [91.1 kB]
Get:359 http://ftpmaster.internal/ubuntu oracular/universe amd64 librhino-java all 1.7.14-2.1 [1330 kB]
Get:360 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhtsjdk-java all 4.1.0+dfsg-1 [1821 kB]
Get:361 http://ftpmaster.internal/ubuntu oracular/universe amd64 libgkl-java all 0.8.11+dfsg-2build1 [24.9 kB]
Get:362 http://ftpmaster.internal/ubuntu oracular/universe amd64 libicu4j-java all 73.2-1 [16.4 MB]
Get:363 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblog4j1.2-java all 1.2.17-11 [439 kB]
Get:364 http://ftpmaster.internal/ubuntu oracular/universe amd64 libicb-utils-java all 2.0.1+git20161002.afee1d9-5 [80.9 kB]
Get:365 http://ftpmaster.internal/ubuntu oracular/main amd64 libice6 amd64 2:1.0.10-1build3 [41.4 kB]
Get:366 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjansi-java all 2.4.1-2 [83.0 kB]
Get:367 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjavassist-java all 1:3.27.0-1 [730 kB]
Get:368 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get:369 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjboss-logging-java all 3.5.3-1 [55.8 kB]
Get:370 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjboss-vfs-java all 3.2.15.Final-3 [129 kB]
Get:371 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjcommander-java all 1.71-4 [68.5 kB]
Get:372 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjsp-api-java all 2.3.4-3 [53.7 kB]
Get:373 http://ftpmaster.internal/ubuntu oracular/universe amd64 libservlet-api-java all 4.0.1-2 [81.0 kB]
Get:374 http://ftpmaster.internal/ubuntu oracular/universe amd64 libwebsocket-api-java all 1.1-2 [40.1 kB]
Get:375 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjetty9-java all 9.4.54-1 [2787 kB]
Get:376 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjsoup-java all 1.15.3-1 [407 kB]
Get:377 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjtidy-java all 7+svn20110807-5 [250 kB]
Get:378 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB]
Get:379 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-antrun-plugin-java all 3.1.0-1 [36.3 kB]
Get:380 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-common-artifact-filters-java all 3.3.2-1 [47.7 kB]
Get:381 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-artifact-transfer-java all 0.13.1-2 [157 kB]
Get:382 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB]
Get:383 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-filtering-java all 3.3.0-1 [49.2 kB]
Get:384 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-assembly-plugin-java all 3.4.2-1 [240 kB]
Get:385 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.0 kB]
Get:386 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-shared-incremental-java all 1.1-4 [9904 B]
Get:387 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-compiler-java all 2.12.1-2 [98.4 kB]
Get:388 http://ftpmaster.internal/ubuntu oracular/universe amd64 libqdox2-java all 2.0.3-1 [296 kB]
Get:389 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-languages-java all 1.1.1-2 [46.8 kB]
Get:390 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-compiler-plugin-java all 3.10.1-2 [58.5 kB]
Get:391 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-dependency-analyzer-java all 1.13.0-1 [30.0 kB]
Get:392 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-dependency-tree-java all 3.2.1-1 [34.1 kB]
Get:393 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-reporting-impl-java all 3.2.0-2 [15.0 kB]
Get:394 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-dependency-plugin-java all 3.5.0-1 [172 kB]
Get:395 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-invoker-java all 3.2.0-1 [27.6 kB]
Get:396 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-interactivity-api-java all 1.1-2 [11.2 kB]
Get:397 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-javadoc-plugin-java all 3.4.1-3 [455 kB]
Get:398 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-container-default1.5-java all 2.1.1-1 [2146 B]
Get:399 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB]
Get:400 http://ftpmaster.internal/ubuntu oracular/universe amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [7872 B]
Get:401 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-plugin-tools-java all 3.7.1-1 [263 kB]
Get:402 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-reporting-exec-java all 1.6.0-1 [26.4 kB]
Get:403 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-resources-plugin-java all 3.3.0-1 [27.9 kB]
Get:404 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-site-plugin-java all 3.12.1-2 [106 kB]
Get:405 http://ftpmaster.internal/ubuntu oracular/universe amd64 libmaven-source-plugin-java all 3.2.1-2 [27.5 kB]
Get:406 http://ftpmaster.internal/ubuntu oracular/main amd64 libpaper1 amd64 1.1.29build1 [13.4 kB]
Get:407 http://ftpmaster.internal/ubuntu oracular/main amd64 libpaper-utils amd64 1.1.29build1 [8650 B]
Get:408 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpicard-java all 3.1.1+dfsg-1 [1731 kB]
Get:409 http://ftpmaster.internal/ubuntu oracular/universe amd64 libpj-java all 0.0~20150107+dfsg-5 [1382 kB]
Get:410 http://ftpmaster.internal/ubuntu oracular/main amd64 libpkgconf3 amd64 1.8.1-2build1 [30.7 kB]
Get:411 http://ftpmaster.internal/ubuntu oracular/main amd64 libprotobuf-lite32t64 amd64 3.21.12-8.2build1 [238 kB]
Get:412 http://ftpmaster.internal/ubuntu oracular/main amd64 libprotobuf32t64 amd64 3.21.12-8.2build1 [923 kB]
Get:413 http://ftpmaster.internal/ubuntu oracular/main amd64 libprotoc32t64 amd64 3.21.12-8.2build1 [683 kB]
Get:414 http://ftpmaster.internal/ubuntu oracular/universe amd64 libreflections-java all 0.10.2+dfsg-2 [124 kB]
Get:415 http://ftpmaster.internal/ubuntu oracular/main amd64 libsm6 amd64 2:1.2.3-1build3 [15.7 kB]
Get:416 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsurefire-java all 2.22.3-2 [1159 kB]
Get:417 http://ftpmaster.internal/ubuntu oracular/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB]
Get:418 http://ftpmaster.internal/ubuntu oracular/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB]
Get:419 http://ftpmaster.internal/ubuntu oracular/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B]
Get:420 http://ftpmaster.internal/ubuntu oracular/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB]
Get:421 http://ftpmaster.internal/ubuntu oracular/universe amd64 libwagon-file-java all 3.5.3-1 [7918 B]
Get:422 http://ftpmaster.internal/ubuntu oracular/universe amd64 libwagon-http-shaded-java all 3.5.3-1 [1332 kB]
Get:423 http://ftpmaster.internal/ubuntu oracular/main amd64 libxml2-utils amd64 2.9.14+dfsg-1.3ubuntu3 [39.4 kB]
Get:424 http://ftpmaster.internal/ubuntu oracular/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB]
Get:425 http://ftpmaster.internal/ubuntu oracular/universe amd64 maven all 3.8.7-2 [18.3 kB]
Get:426 http://ftpmaster.internal/ubuntu oracular/universe amd64 maven-repo-helper all 1.11 [137 kB]
Get:427 http://ftpmaster.internal/ubuntu oracular/universe amd64 maven-debian-helper all 2.6.4 [107 kB]
Get:428 http://ftpmaster.internal/ubuntu oracular/main amd64 pkgconf-bin amd64 1.8.1-2build1 [20.7 kB]
Get:429 http://ftpmaster.internal/ubuntu oracular/main amd64 pkgconf amd64 1.8.1-2build1 [16.8 kB]
Get:430 http://ftpmaster.internal/ubuntu oracular/main amd64 zip amd64 3.0-13build1 [175 kB]
Get:431 http://ftpmaster.internal/ubuntu oracular/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB]
Get:432 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 r-base-core amd64 4.4.0-2 [28.5 MB]
Get:433 http://ftpmaster.internal/ubuntu oracular/universe amd64 r-cran-rjava amd64 1.0-11-1 [711 kB]
Get:434 http://ftpmaster.internal/ubuntu oracular/universe amd64 testng all 6.9.12-4 [773 kB]
Get:435 http://ftpmaster.internal/ubuntu oracular/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1ubuntu2 [894 kB]
Get:436 http://ftpmaster.internal/ubuntu oracular/universe amd64 ant-contrib all 1.0~b3+svn177-12 [262 kB]
Get:437 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjbzip2-java all 0.9.1-8 [42.4 kB]
Get:438 http://ftpmaster.internal/ubuntu oracular/main amd64 libprotobuf-dev amd64 3.21.12-8.2build1 [1414 kB]
Get:439 http://ftpmaster.internal/ubuntu oracular/universe amd64 libprotobuf-java all 3.21.12-8.2build1 [1208 kB]
Get:440 http://ftpmaster.internal/ubuntu oracular/universe amd64 protobuf-compiler amd64 3.21.12-8.2build1 [29.0 kB]
Preconfiguring packages ...
Fetched 381 MB in 4s (88.1 MB/s)
Selecting previously unselected package libpython3.12-minimal:amd64.
(Reading database ... 16045 files and directories currently installed.)
Preparing to unpack .../libpython3.12-minimal_3.12.3-1_amd64.deb ...
Unpacking libpython3.12-minimal:amd64 (3.12.3-1) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.6.2-1) ...
Selecting previously unselected package python3.12-minimal.
Preparing to unpack .../python3.12-minimal_3.12.3-1_amd64.deb ...
Unpacking python3.12-minimal (3.12.3-1) ...
Setting up libpython3.12-minimal:amd64 (3.12.3-1) ...
Setting up libexpat1:amd64 (2.6.2-1) ...
Setting up python3.12-minimal (3.12.3-1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 16363 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.12.3-0ubuntu1_amd64.deb ...
Unpacking python3-minimal (3.12.3-0ubuntu1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_10.1.0_all.deb ...
Unpacking media-types (10.1.0) ...
Selecting previously unselected package netbase.
Preparing to unpack .../2-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package libpython3.12-stdlib:amd64.
Preparing to unpack .../3-libpython3.12-stdlib_3.12.3-1_amd64.deb ...
Unpacking libpython3.12-stdlib:amd64 (3.12.3-1) ...
Selecting previously unselected package python3.12.
Preparing to unpack .../4-python3.12_3.12.3-1_amd64.deb ...
Unpacking python3.12 (3.12.3-1) ...
Selecting previously unselected package libpython3-stdlib:amd64.
Preparing to unpack .../5-libpython3-stdlib_3.12.3-0ubuntu1_amd64.deb ...
Unpacking libpython3-stdlib:amd64 (3.12.3-0ubuntu1) ...
Setting up python3-minimal (3.12.3-0ubuntu1) ...
Selecting previously unselected package python3.
(Reading database ... 16804 files and directories currently installed.)
Preparing to unpack .../000-python3_3.12.3-0ubuntu1_amd64.deb ...
Unpacking python3 (3.12.3-0ubuntu1) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../001-libpipeline1_1.5.7-2_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.7-2) ...
Selecting previously unselected package binfmt-support.
Preparing to unpack .../002-binfmt-support_2.2.2-7_amd64.deb ...
Unpacking binfmt-support (2.2.2-7) ...
Selecting previously unselected package sgml-base.
Preparing to unpack .../003-sgml-base_1.31_all.deb ...
Unpacking sgml-base (1.31) ...
Selecting previously unselected package libdbus-1-3:amd64.
Preparing to unpack .../004-libdbus-1-3_1.14.10-4ubuntu4_amd64.deb ...
Unpacking libdbus-1-3:amd64 (1.14.10-4ubuntu4) ...
Selecting previously unselected package dbus-bin.
Preparing to unpack .../005-dbus-bin_1.14.10-4ubuntu4_amd64.deb ...
Unpacking dbus-bin (1.14.10-4ubuntu4) ...
Selecting previously unselected package dbus-session-bus-common.
Preparing to unpack .../006-dbus-session-bus-common_1.14.10-4ubuntu4_all.deb ...
Unpacking dbus-session-bus-common (1.14.10-4ubuntu4) ...
Selecting previously unselected package dbus-daemon.
Preparing to unpack .../007-dbus-daemon_1.14.10-4ubuntu4_amd64.deb ...
Unpacking dbus-daemon (1.14.10-4ubuntu4) ...
Selecting previously unselected package dbus-system-bus-common.
Preparing to unpack .../008-dbus-system-bus-common_1.14.10-4ubuntu4_all.deb ...
Unpacking dbus-system-bus-common (1.14.10-4ubuntu4) ...
Selecting previously unselected package dbus.
Preparing to unpack .../009-dbus_1.14.10-4ubuntu4_amd64.deb ...
Unpacking dbus (1.14.10-4ubuntu4) ...
Selecting previously unselected package libpam-systemd:amd64.
Preparing to unpack .../010-libpam-systemd_256~rc1-1~exp2ubuntu1_amd64.deb ...
Unpacking libpam-systemd:amd64 (256~rc1-1~exp2ubuntu1) ...
Selecting previously unselected package dbus-user-session.
Preparing to unpack .../011-dbus-user-session_1.14.10-4ubuntu4_amd64.deb ...
Unpacking dbus-user-session (1.14.10-4ubuntu4) ...
Selecting previously unselected package libbsd0:amd64.
Preparing to unpack .../012-libbsd0_0.12.2-1_amd64.deb ...
Unpacking libbsd0:amd64 (0.12.2-1) ...
Selecting previously unselected package libelf1t64:amd64.
Preparing to unpack .../013-libelf1t64_0.191-1_amd64.deb ...
Unpacking libelf1t64:amd64 (0.191-1) ...
Selecting previously unselected package libfribidi0:amd64.
Preparing to unpack .../014-libfribidi0_1.0.13-3build1_amd64.deb ...
Unpacking libfribidi0:amd64 (1.0.13-3build1) ...
Selecting previously unselected package libglib2.0-0t64:amd64.
Preparing to unpack .../015-libglib2.0-0t64_2.80.1-0ubuntu2_amd64.deb ...
Unpacking libglib2.0-0t64:amd64 (2.80.1-0ubuntu2) ...
Selecting previously unselected package libicu74:amd64.
Preparing to unpack .../016-libicu74_74.2-1ubuntu3_amd64.deb ...
Unpacking libicu74:amd64 (74.2-1ubuntu3) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../017-libxml2_2.9.14+dfsg-1.3ubuntu3_amd64.deb ...
Unpacking libxml2:amd64 (2.9.14+dfsg-1.3ubuntu3) ...
Selecting previously unselected package shared-mime-info.
Preparing to unpack .../018-shared-mime-info_2.4-4_amd64.deb ...
Unpacking shared-mime-info (2.4-4) ...
Selecting previously unselected package ucf.
Preparing to unpack .../019-ucf_3.0043+nmu1_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0043+nmu1) ...
Selecting previously unselected package xkb-data.
Preparing to unpack .../020-xkb-data_2.41-2ubuntu1_all.deb ...
Unpacking xkb-data (2.41-2ubuntu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../021-libmagic-mgc_1%3a5.45-3build1_amd64.deb ...
Unpacking libmagic-mgc (1:5.45-3build1) ...
Selecting previously unselected package libmagic1t64:amd64.
Preparing to unpack .../022-libmagic1t64_1%3a5.45-3build1_amd64.deb ...
Unpacking libmagic1t64:amd64 (1:5.45-3build1) ...
Selecting previously unselected package file.
Preparing to unpack .../023-file_1%3a5.45-3build1_amd64.deb ...
Unpacking file (1:5.45-3build1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../024-gettext-base_0.21-14ubuntu2_amd64.deb ...
Unpacking gettext-base (0.21-14ubuntu2) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../025-libuchardet0_0.0.8-1build1_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.8-1build1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../026-groff-base_1.23.0-4_amd64.deb ...
Unpacking groff-base (1.23.0-4) ...
Selecting previously unselected package libdrm-common.
Preparing to unpack .../027-libdrm-common_2.4.120-2build1_all.deb ...
Unpacking libdrm-common (2.4.120-2build1) ...
Selecting previously unselected package libdrm2:amd64.
Preparing to unpack .../028-libdrm2_2.4.120-2build1_amd64.deb ...
Unpacking libdrm2:amd64 (2.4.120-2build1) ...
Selecting previously unselected package libedit2:amd64.
Preparing to unpack .../029-libedit2_3.1-20230828-1build1_amd64.deb ...
Unpacking libedit2:amd64 (3.1-20230828-1build1) ...
Selecting previously unselected package libnghttp2-14:amd64.
Preparing to unpack .../030-libnghttp2-14_1.61.0-1_amd64.deb ...
Unpacking libnghttp2-14:amd64 (1.61.0-1) ...
Selecting previously unselected package libpsl5t64:amd64.
Preparing to unpack .../031-libpsl5t64_0.21.2-1.1build1_amd64.deb ...
Unpacking libpsl5t64:amd64 (0.21.2-1.1build1) ...
Selecting previously unselected package libsensors-config.
Preparing to unpack .../032-libsensors-config_1%3a3.6.0-9build1_all.deb ...
Unpacking libsensors-config (1:3.6.0-9build1) ...
Selecting previously unselected package libsensors5:amd64.
Preparing to unpack .../033-libsensors5_1%3a3.6.0-9build1_amd64.deb ...
Unpacking libsensors5:amd64 (1:3.6.0-9build1) ...
Selecting previously unselected package libxau6:amd64.
Preparing to unpack .../034-libxau6_1%3a1.0.9-1build6_amd64.deb ...
Unpacking libxau6:amd64 (1:1.0.9-1build6) ...
Selecting previously unselected package libxdmcp6:amd64.
Preparing to unpack .../035-libxdmcp6_1%3a1.1.3-0ubuntu6_amd64.deb ...
Unpacking libxdmcp6:amd64 (1:1.1.3-0ubuntu6) ...
Selecting previously unselected package libxcb1:amd64.
Preparing to unpack .../036-libxcb1_1.15-1ubuntu2_amd64.deb ...
Unpacking libxcb1:amd64 (1.15-1ubuntu2) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../037-libx11-data_2%3a1.8.7-1build1_all.deb ...
Unpacking libx11-data (2:1.8.7-1build1) ...
Selecting previously unselected package libx11-6:amd64.
Preparing to unpack .../038-libx11-6_2%3a1.8.7-1build1_amd64.deb ...
Unpacking libx11-6:amd64 (2:1.8.7-1build1) ...
Selecting previously unselected package libxext6:amd64.
Preparing to unpack .../039-libxext6_2%3a1.3.4-1build2_amd64.deb ...
Unpacking libxext6:amd64 (2:1.3.4-1build2) ...
Selecting previously unselected package libxkbcommon0:amd64.
Preparing to unpack .../040-libxkbcommon0_1.6.0-1build1_amd64.deb ...
Unpacking libxkbcommon0:amd64 (1.6.0-1build1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../041-man-db_2.12.1-1_amd64.deb ...
Unpacking man-db (2.12.1-1) ...
Selecting previously unselected package libgdk-pixbuf2.0-common.
Preparing to unpack .../042-libgdk-pixbuf2.0-common_2.42.10+dfsg-3ubuntu3_all.deb ...
Unpacking libgdk-pixbuf2.0-common (2.42.10+dfsg-3ubuntu3) ...
Selecting previously unselected package libjpeg-turbo8:amd64.
Preparing to unpack .../043-libjpeg-turbo8_2.1.5-2ubuntu2_amd64.deb ...
Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ...
Selecting previously unselected package libjpeg8:amd64.
Preparing to unpack .../044-libjpeg8_8c-2ubuntu11_amd64.deb ...
Unpacking libjpeg8:amd64 (8c-2ubuntu11) ...
Selecting previously unselected package libdeflate0:amd64.
Preparing to unpack .../045-libdeflate0_1.20-1_amd64.deb ...
Unpacking libdeflate0:amd64 (1.20-1) ...
Selecting previously unselected package libjbig0:amd64.
Preparing to unpack .../046-libjbig0_2.1-6.1ubuntu2_amd64.deb ...
Unpacking libjbig0:amd64 (2.1-6.1ubuntu2) ...
Selecting previously unselected package liblerc4:amd64.
Preparing to unpack .../047-liblerc4_4.0.0+ds-4ubuntu2_amd64.deb ...
Unpacking liblerc4:amd64 (4.0.0+ds-4ubuntu2) ...
Selecting previously unselected package libsharpyuv0:amd64.
Preparing to unpack .../048-libsharpyuv0_1.4.0-0.1_amd64.deb ...
Unpacking libsharpyuv0:amd64 (1.4.0-0.1) ...
Selecting previously unselected package libwebp7:amd64.
Preparing to unpack .../049-libwebp7_1.4.0-0.1_amd64.deb ...
Unpacking libwebp7:amd64 (1.4.0-0.1) ...
Selecting previously unselected package libtiff6:amd64.
Preparing to unpack .../050-libtiff6_4.5.1+git230720-4ubuntu2_amd64.deb ...
Unpacking libtiff6:amd64 (4.5.1+git230720-4ubuntu2) ...
Selecting previously unselected package libgdk-pixbuf-2.0-0:amd64.
Preparing to unpack .../051-libgdk-pixbuf-2.0-0_2.42.10+dfsg-3ubuntu3_amd64.deb ...
Unpacking libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3ubuntu3) ...
Selecting previously unselected package gtk-update-icon-cache.
Preparing to unpack .../052-gtk-update-icon-cache_3.24.41-4ubuntu1_amd64.deb ...
Unpacking gtk-update-icon-cache (3.24.41-4ubuntu1) ...
Selecting previously unselected package hicolor-icon-theme.
Preparing to unpack .../053-hicolor-icon-theme_0.17-2_all.deb ...
Unpacking hicolor-icon-theme (0.17-2) ...
Selecting previously unselected package humanity-icon-theme.
Preparing to unpack .../054-humanity-icon-theme_0.6.16_all.deb ...
Unpacking humanity-icon-theme (0.6.16) ...
Selecting previously unselected package ubuntu-mono.
Preparing to unpack .../055-ubuntu-mono_24.04-0ubuntu1_all.deb ...
Unpacking ubuntu-mono (24.04-0ubuntu1) ...
Selecting previously unselected package adwaita-icon-theme.
Preparing to unpack .../056-adwaita-icon-theme_46.0-1_all.deb ...
Unpacking adwaita-icon-theme (46.0-1) ...
Selecting previously unselected package ca-certificates-java.
Preparing to unpack .../057-ca-certificates-java_20240118_all.deb ...
Unpacking ca-certificates-java (20240118) ...
Selecting previously unselected package java-common.
Preparing to unpack .../058-java-common_0.75+exp1_all.deb ...
Unpacking java-common (0.75+exp1) ...
Selecting previously unselected package liblcms2-2:amd64.
Preparing to unpack .../059-liblcms2-2_2.14-2build1_amd64.deb ...
Unpacking liblcms2-2:amd64 (2.14-2build1) ...
Selecting previously unselected package libnspr4:amd64.
Preparing to unpack .../060-libnspr4_2%3a4.35-1.1build1_amd64.deb ...
Unpacking libnspr4:amd64 (2:4.35-1.1build1) ...
Selecting previously unselected package libnss3:amd64.
Preparing to unpack .../061-libnss3_2%3a3.99-1_amd64.deb ...
Unpacking libnss3:amd64 (2:3.99-1) ...
Selecting previously unselected package libpcsclite1:amd64.
Preparing to unpack .../062-libpcsclite1_2.2.1-1_amd64.deb ...
Unpacking libpcsclite1:amd64 (2.2.1-1) ...
Selecting previously unselected package openjdk-21-jre-headless:amd64.
Preparing to unpack .../063-openjdk-21-jre-headless_21.0.3+9-1ubuntu1_amd64.deb ...
Unpacking openjdk-21-jre-headless:amd64 (21.0.3+9-1ubuntu1) ...
Selecting previously unselected package default-jre-headless.
Preparing to unpack .../064-default-jre-headless_2%3a1.21-75+exp1_amd64.deb ...
Unpacking default-jre-headless (2:1.21-75+exp1) ...
Selecting previously unselected package ant.
Preparing to unpack .../065-ant_1.10.14-1_all.deb ...
Unpacking ant (1.10.14-1) ...
Selecting previously unselected package at-spi2-common.
Preparing to unpack .../066-at-spi2-common_2.52.0-1build1_all.deb ...
Unpacking at-spi2-common (2.52.0-1build1) ...
Selecting previously unselected package m4.
Preparing to unpack .../067-m4_1.4.19-4build1_amd64.deb ...
Unpacking m4 (1.4.19-4build1) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../068-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../069-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../070-automake_1%3a1.16.5-1.3ubuntu1_all.deb ...
Unpacking automake (1:1.16.5-1.3ubuntu1) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../071-autopoint_0.21-14ubuntu2_all.deb ...
Unpacking autopoint (0.21-14ubuntu2) ...
Selecting previously unselected package libdconf1:amd64.
Preparing to unpack .../072-libdconf1_0.40.0-4build2_amd64.deb ...
Unpacking libdconf1:amd64 (0.40.0-4build2) ...
Selecting previously unselected package dconf-service.
Preparing to unpack .../073-dconf-service_0.40.0-4build2_amd64.deb ...
Unpacking dconf-service (0.40.0-4build2) ...
Selecting previously unselected package dconf-gsettings-backend:amd64.
Preparing to unpack .../074-dconf-gsettings-backend_0.40.0-4build2_amd64.deb ...
Unpacking dconf-gsettings-backend:amd64 (0.40.0-4build2) ...
Selecting previously unselected package dctrl-tools.
Preparing to unpack .../075-dctrl-tools_2.24-3build3_amd64.deb ...
Unpacking dctrl-tools (2.24-3build3) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../076-libdebhelper-perl_13.14.1ubuntu5_all.deb ...
Unpacking libdebhelper-perl (13.14.1ubuntu5) ...
Selecting previously unselected package libtool.
Preparing to unpack .../077-libtool_2.4.7-7build1_all.deb ...
Unpacking libtool (2.4.7-7build1) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../078-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../079-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../080-libsub-override-perl_0.10-1_all.deb ...
Unpacking libsub-override-perl (0.10-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../081-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../082-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libdw1t64:amd64.
Preparing to unpack .../083-libdw1t64_0.191-1_amd64.deb ...
Unpacking libdw1t64:amd64 (0.191-1) ...
Selecting previously unselected package debugedit.
Preparing to unpack .../084-debugedit_1%3a5.0-5build2_amd64.deb ...
Unpacking debugedit (1:5.0-5build2) ...
Selecting previously unselected package dwz.
Preparing to unpack .../085-dwz_0.15-1build6_amd64.deb ...
Unpacking dwz (0.15-1build6) ...
Selecting previously unselected package gettext.
Preparing to unpack .../086-gettext_0.21-14ubuntu2_amd64.deb ...
Unpacking gettext (0.21-14ubuntu2) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../087-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../088-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../089-debhelper_13.14.1ubuntu5_all.deb ...
Unpacking debhelper (13.14.1ubuntu5) ...
Selecting previously unselected package libatk1.0-0t64:amd64.
Preparing to unpack .../090-libatk1.0-0t64_2.52.0-1build1_amd64.deb ...
Unpacking libatk1.0-0t64:amd64 (2.52.0-1build1) ...
Selecting previously unselected package libxi6:amd64.
Preparing to unpack .../091-libxi6_2%3a1.8.1-1build1_amd64.deb ...
Unpacking libxi6:amd64 (2:1.8.1-1build1) ...
Selecting previously unselected package libatspi2.0-0t64:amd64.
Preparing to unpack .../092-libatspi2.0-0t64_2.52.0-1build1_amd64.deb ...
Unpacking libatspi2.0-0t64:amd64 (2.52.0-1build1) ...
Selecting previously unselected package libatk-bridge2.0-0t64:amd64.
Preparing to unpack .../093-libatk-bridge2.0-0t64_2.52.0-1build1_amd64.deb ...
Unpacking libatk-bridge2.0-0t64:amd64 (2.52.0-1build1) ...
Selecting previously unselected package libbrotli1:amd64.
Preparing to unpack .../094-libbrotli1_1.1.0-2build2_amd64.deb ...
Unpacking libbrotli1:amd64 (1.1.0-2build2) ...
Selecting previously unselected package libfreetype6:amd64.
Preparing to unpack .../095-libfreetype6_2.13.2+dfsg-1build3_amd64.deb ...
Unpacking libfreetype6:amd64 (2.13.2+dfsg-1build3) ...
Selecting previously unselected package fonts-dejavu-mono.
Preparing to unpack .../096-fonts-dejavu-mono_2.37-8_all.deb ...
Unpacking fonts-dejavu-mono (2.37-8) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../097-fonts-dejavu-core_2.37-8_all.deb ...
Unpacking fonts-dejavu-core (2.37-8) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../098-fontconfig-config_2.15.0-1.1ubuntu2_amd64.deb ...
Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
Selecting previously unselected package libfontconfig1:amd64.
Preparing to unpack .../099-libfontconfig1_2.15.0-1.1ubuntu2_amd64.deb ...
Unpacking libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
Selecting previously unselected package libpixman-1-0:amd64.
Preparing to unpack .../100-libpixman-1-0_0.42.2-1build1_amd64.deb ...
Unpacking libpixman-1-0:amd64 (0.42.2-1build1) ...
Selecting previously unselected package libxcb-render0:amd64.
Preparing to unpack .../101-libxcb-render0_1.15-1ubuntu2_amd64.deb ...
Unpacking libxcb-render0:amd64 (1.15-1ubuntu2) ...
Selecting previously unselected package libxcb-shm0:amd64.
Preparing to unpack .../102-libxcb-shm0_1.15-1ubuntu2_amd64.deb ...
Unpacking libxcb-shm0:amd64 (1.15-1ubuntu2) ...
Selecting previously unselected package libxrender1:amd64.
Preparing to unpack .../103-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ...
Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ...
Selecting previously unselected package libcairo2:amd64.
Preparing to unpack .../104-libcairo2_1.18.0-3build1_amd64.deb ...
Unpacking libcairo2:amd64 (1.18.0-3build1) ...
Selecting previously unselected package libcairo-gobject2:amd64.
Preparing to unpack .../105-libcairo-gobject2_1.18.0-3build1_amd64.deb ...
Unpacking libcairo-gobject2:amd64 (1.18.0-3build1) ...
Selecting previously unselected package libcolord2:amd64.
Preparing to unpack .../106-libcolord2_1.4.7-1build2_amd64.deb ...
Unpacking libcolord2:amd64 (1.4.7-1build2) ...
Selecting previously unselected package libavahi-common-data:amd64.
Preparing to unpack .../107-libavahi-common-data_0.8-13ubuntu6_amd64.deb ...
Unpacking libavahi-common-data:amd64 (0.8-13ubuntu6) ...
Selecting previously unselected package libavahi-common3:amd64.
Preparing to unpack .../108-libavahi-common3_0.8-13ubuntu6_amd64.deb ...
Unpacking libavahi-common3:amd64 (0.8-13ubuntu6) ...
Selecting previously unselected package libavahi-client3:amd64.
Preparing to unpack .../109-libavahi-client3_0.8-13ubuntu6_amd64.deb ...
Unpacking libavahi-client3:amd64 (0.8-13ubuntu6) ...
Selecting previously unselected package libcups2t64:amd64.
Preparing to unpack .../110-libcups2t64_2.4.7-1.2ubuntu7_amd64.deb ...
Unpacking libcups2t64:amd64 (2.4.7-1.2ubuntu7) ...
Selecting previously unselected package libepoxy0:amd64.
Preparing to unpack .../111-libepoxy0_1.5.10-1build1_amd64.deb ...
Unpacking libepoxy0:amd64 (1.5.10-1build1) ...
Selecting previously unselected package libgraphite2-3:amd64.
Preparing to unpack .../112-libgraphite2-3_1.3.14-2build1_amd64.deb ...
Unpacking libgraphite2-3:amd64 (1.3.14-2build1) ...
Selecting previously unselected package libharfbuzz0b:amd64.
Preparing to unpack .../113-libharfbuzz0b_8.3.0-2build2_amd64.deb ...
Unpacking libharfbuzz0b:amd64 (8.3.0-2build2) ...
Selecting previously unselected package fontconfig.
Preparing to unpack .../114-fontconfig_2.15.0-1.1ubuntu2_amd64.deb ...
Unpacking fontconfig (2.15.0-1.1ubuntu2) ...
Selecting previously unselected package libthai-data.
Preparing to unpack .../115-libthai-data_0.1.29-2build1_all.deb ...
Unpacking libthai-data (0.1.29-2build1) ...
Selecting previously unselected package libdatrie1:amd64.
Preparing to unpack .../116-libdatrie1_0.2.13-3build1_amd64.deb ...
Unpacking libdatrie1:amd64 (0.2.13-3build1) ...
Selecting previously unselected package libthai0:amd64.
Preparing to unpack .../117-libthai0_0.1.29-2build1_amd64.deb ...
Unpacking libthai0:amd64 (0.1.29-2build1) ...
Selecting previously unselected package libpango-1.0-0:amd64.
Preparing to unpack .../118-libpango-1.0-0_1.52.2+ds-1_amd64.deb ...
Unpacking libpango-1.0-0:amd64 (1.52.2+ds-1) ...
Selecting previously unselected package libpangoft2-1.0-0:amd64.
Preparing to unpack .../119-libpangoft2-1.0-0_1.52.2+ds-1_amd64.deb ...
Unpacking libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ...
Selecting previously unselected package libpangocairo-1.0-0:amd64.
Preparing to unpack .../120-libpangocairo-1.0-0_1.52.2+ds-1_amd64.deb ...
Unpacking libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ...
Selecting previously unselected package libwayland-client0:amd64.
Preparing to unpack .../121-libwayland-client0_1.22.0-2.1build1_amd64.deb ...
Unpacking libwayland-client0:amd64 (1.22.0-2.1build1) ...
Selecting previously unselected package libwayland-cursor0:amd64.
Preparing to unpack .../122-libwayland-cursor0_1.22.0-2.1build1_amd64.deb ...
Unpacking libwayland-cursor0:amd64 (1.22.0-2.1build1) ...
Selecting previously unselected package libwayland-egl1:amd64.
Preparing to unpack .../123-libwayland-egl1_1.22.0-2.1build1_amd64.deb ...
Unpacking libwayland-egl1:amd64 (1.22.0-2.1build1) ...
Selecting previously unselected package libxcomposite1:amd64.
Preparing to unpack .../124-libxcomposite1_1%3a0.4.5-1build3_amd64.deb ...
Unpacking libxcomposite1:amd64 (1:0.4.5-1build3) ...
Selecting previously unselected package libxfixes3:amd64.
Preparing to unpack .../125-libxfixes3_1%3a6.0.0-2build1_amd64.deb ...
Unpacking libxfixes3:amd64 (1:6.0.0-2build1) ...
Selecting previously unselected package libxcursor1:amd64.
Preparing to unpack .../126-libxcursor1_1%3a1.2.1-1build1_amd64.deb ...
Unpacking libxcursor1:amd64 (1:1.2.1-1build1) ...
Selecting previously unselected package libxdamage1:amd64.
Preparing to unpack .../127-libxdamage1_1%3a1.1.6-1build1_amd64.deb ...
Unpacking libxdamage1:amd64 (1:1.1.6-1build1) ...
Selecting previously unselected package libxinerama1:amd64.
Preparing to unpack .../128-libxinerama1_2%3a1.1.4-3build1_amd64.deb ...
Unpacking libxinerama1:amd64 (2:1.1.4-3build1) ...
Selecting previously unselected package libxrandr2:amd64.
Preparing to unpack .../129-libxrandr2_2%3a1.5.4-1_amd64.deb ...
Unpacking libxrandr2:amd64 (2:1.5.4-1) ...
Selecting previously unselected package libgtk-3-common.
Preparing to unpack .../130-libgtk-3-common_3.24.41-4ubuntu1_all.deb ...
Unpacking libgtk-3-common (3.24.41-4ubuntu1) ...
Selecting previously unselected package libgtk-3-0t64:amd64.
Preparing to unpack .../131-libgtk-3-0t64_3.24.41-4ubuntu1_amd64.deb ...
Unpacking libgtk-3-0t64:amd64 (3.24.41-4ubuntu1) ...
Selecting previously unselected package libglvnd0:amd64.
Preparing to unpack .../132-libglvnd0_1.7.0-1build1_amd64.deb ...
Unpacking libglvnd0:amd64 (1.7.0-1build1) ...
Selecting previously unselected package libglapi-mesa:amd64.
Preparing to unpack .../133-libglapi-mesa_24.0.7-1ubuntu1_amd64.deb ...
Unpacking libglapi-mesa:amd64 (24.0.7-1ubuntu1) ...
Selecting previously unselected package libx11-xcb1:amd64.
Preparing to unpack .../134-libx11-xcb1_2%3a1.8.7-1build1_amd64.deb ...
Unpacking libx11-xcb1:amd64 (2:1.8.7-1build1) ...
Selecting previously unselected package libxcb-dri2-0:amd64.
Preparing to unpack .../135-libxcb-dri2-0_1.15-1ubuntu2_amd64.deb ...
Unpacking libxcb-dri2-0:amd64 (1.15-1ubuntu2) ...
Selecting previously unselected package libxcb-dri3-0:amd64.
Preparing to unpack .../136-libxcb-dri3-0_1.15-1ubuntu2_amd64.deb ...
Unpacking libxcb-dri3-0:amd64 (1.15-1ubuntu2) ...
Selecting previously unselected package libxcb-glx0:amd64.
Preparing to unpack .../137-libxcb-glx0_1.15-1ubuntu2_amd64.deb ...
Unpacking libxcb-glx0:amd64 (1.15-1ubuntu2) ...
Selecting previously unselected package libxcb-present0:amd64.
Preparing to unpack .../138-libxcb-present0_1.15-1ubuntu2_amd64.deb ...
Unpacking libxcb-present0:amd64 (1.15-1ubuntu2) ...
Selecting previously unselected package libxcb-randr0:amd64.
Preparing to unpack .../139-libxcb-randr0_1.15-1ubuntu2_amd64.deb ...
Unpacking libxcb-randr0:amd64 (1.15-1ubuntu2) ...
Selecting previously unselected package libxcb-sync1:amd64.
Preparing to unpack .../140-libxcb-sync1_1.15-1ubuntu2_amd64.deb ...
Unpacking libxcb-sync1:amd64 (1.15-1ubuntu2) ...
Selecting previously unselected package libxcb-xfixes0:amd64.
Preparing to unpack .../141-libxcb-xfixes0_1.15-1ubuntu2_amd64.deb ...
Unpacking libxcb-xfixes0:amd64 (1.15-1ubuntu2) ...
Selecting previously unselected package libxshmfence1:amd64.
Preparing to unpack .../142-libxshmfence1_1.3-1build5_amd64.deb ...
Unpacking libxshmfence1:amd64 (1.3-1build5) ...
Selecting previously unselected package libxxf86vm1:amd64.
Preparing to unpack .../143-libxxf86vm1_1%3a1.1.4-1build4_amd64.deb ...
Unpacking libxxf86vm1:amd64 (1:1.1.4-1build4) ...
Selecting previously unselected package libvulkan1:amd64.
Preparing to unpack .../144-libvulkan1_1.3.280.0-1_amd64.deb ...
Unpacking libvulkan1:amd64 (1.3.280.0-1) ...
Selecting previously unselected package libdrm-amdgpu1:amd64.
Preparing to unpack .../145-libdrm-amdgpu1_2.4.120-2build1_amd64.deb ...
Unpacking libdrm-amdgpu1:amd64 (2.4.120-2build1) ...
Selecting previously unselected package libpciaccess0:amd64.
Preparing to unpack .../146-libpciaccess0_0.17-3build1_amd64.deb ...
Unpacking libpciaccess0:amd64 (0.17-3build1) ...
Selecting previously unselected package libdrm-intel1:amd64.
Preparing to unpack .../147-libdrm-intel1_2.4.120-2build1_amd64.deb ...
Unpacking libdrm-intel1:amd64 (2.4.120-2build1) ...
Selecting previously unselected package libdrm-nouveau2:amd64.
Preparing to unpack .../148-libdrm-nouveau2_2.4.120-2build1_amd64.deb ...
Unpacking libdrm-nouveau2:amd64 (2.4.120-2build1) ...
Selecting previously unselected package libdrm-radeon1:amd64.
Preparing to unpack .../149-libdrm-radeon1_2.4.120-2build1_amd64.deb ...
Unpacking libdrm-radeon1:amd64 (2.4.120-2build1) ...
Selecting previously unselected package libllvm17t64:amd64.
Preparing to unpack .../150-libllvm17t64_1%3a17.0.6-12_amd64.deb ...
Unpacking libllvm17t64:amd64 (1:17.0.6-12) ...
Selecting previously unselected package libgl1-mesa-dri:amd64.
Preparing to unpack .../151-libgl1-mesa-dri_24.0.7-1ubuntu1_amd64.deb ...
Unpacking libgl1-mesa-dri:amd64 (24.0.7-1ubuntu1) ...
Selecting previously unselected package libglx-mesa0:amd64.
Preparing to unpack .../152-libglx-mesa0_24.0.7-1ubuntu1_amd64.deb ...
Unpacking libglx-mesa0:amd64 (24.0.7-1ubuntu1) ...
Selecting previously unselected package libglx0:amd64.
Preparing to unpack .../153-libglx0_1.7.0-1build1_amd64.deb ...
Unpacking libglx0:amd64 (1.7.0-1build1) ...
Selecting previously unselected package libgl1:amd64.
Preparing to unpack .../154-libgl1_1.7.0-1build1_amd64.deb ...
Unpacking libgl1:amd64 (1.7.0-1build1) ...
Selecting previously unselected package libasound2-data.
Preparing to unpack .../155-libasound2-data_1.2.11-1build2_all.deb ...
Unpacking libasound2-data (1.2.11-1build2) ...
Selecting previously unselected package libasound2t64:amd64.
Preparing to unpack .../156-libasound2t64_1.2.11-1build2_amd64.deb ...
Unpacking libasound2t64:amd64 (1.2.11-1build2) ...
Selecting previously unselected package libgif7:amd64.
Preparing to unpack .../157-libgif7_5.2.2-1ubuntu1_amd64.deb ...
Unpacking libgif7:amd64 (5.2.2-1ubuntu1) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../158-x11-common_1%3a7.7+23ubuntu3_all.deb ...
Unpacking x11-common (1:7.7+23ubuntu3) ...
Selecting previously unselected package libxtst6:amd64.
Preparing to unpack .../159-libxtst6_2%3a1.2.3-1.1build1_amd64.deb ...
Unpacking libxtst6:amd64 (2:1.2.3-1.1build1) ...
Selecting previously unselected package openjdk-21-jre:amd64.
Preparing to unpack .../160-openjdk-21-jre_21.0.3+9-1ubuntu1_amd64.deb ...
Unpacking openjdk-21-jre:amd64 (21.0.3+9-1ubuntu1) ...
Selecting previously unselected package default-jre.
Preparing to unpack .../161-default-jre_2%3a1.21-75+exp1_amd64.deb ...
Unpacking default-jre (2:1.21-75+exp1) ...
Selecting previously unselected package openjdk-21-jdk-headless:amd64.
Preparing to unpack .../162-openjdk-21-jdk-headless_21.0.3+9-1ubuntu1_amd64.deb ...
Unpacking openjdk-21-jdk-headless:amd64 (21.0.3+9-1ubuntu1) ...
Selecting previously unselected package default-jdk-headless.
Preparing to unpack .../163-default-jdk-headless_2%3a1.21-75+exp1_amd64.deb ...
Unpacking default-jdk-headless (2:1.21-75+exp1) ...
Selecting previously unselected package openjdk-21-jdk:amd64.
Preparing to unpack .../164-openjdk-21-jdk_21.0.3+9-1ubuntu1_amd64.deb ...
Unpacking openjdk-21-jdk:amd64 (21.0.3+9-1ubuntu1) ...
Selecting previously unselected package default-jdk.
Preparing to unpack .../165-default-jdk_2%3a1.21-75+exp1_amd64.deb ...
Unpacking default-jdk (2:1.21-75+exp1) ...
Selecting previously unselected package libksba8:amd64.
Preparing to unpack .../166-libksba8_1.6.6-1build1_amd64.deb ...
Unpacking libksba8:amd64 (1.6.6-1build1) ...
Selecting previously unselected package libsasl2-modules-db:amd64.
Preparing to unpack .../167-libsasl2-modules-db_2.1.28+dfsg1-5ubuntu3_amd64.deb ...
Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-5ubuntu3) ...
Selecting previously unselected package libsasl2-2:amd64.
Preparing to unpack .../168-libsasl2-2_2.1.28+dfsg1-5ubuntu3_amd64.deb ...
Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-5ubuntu3) ...
Selecting previously unselected package libldap2:amd64.
Preparing to unpack .../169-libldap2_2.6.7+dfsg-1~exp1ubuntu8_amd64.deb ...
Unpacking libldap2:amd64 (2.6.7+dfsg-1~exp1ubuntu8) ...
Selecting previously unselected package dirmngr.
Preparing to unpack .../170-dirmngr_2.4.4-2ubuntu17_amd64.deb ...
Unpacking dirmngr (2.4.4-2ubuntu17) ...
Selecting previously unselected package gnupg-utils.
Preparing to unpack .../171-gnupg-utils_2.4.4-2ubuntu17_amd64.deb ...
Unpacking gnupg-utils (2.4.4-2ubuntu17) ...
Selecting previously unselected package gpgsm.
Preparing to unpack .../172-gpgsm_2.4.4-2ubuntu17_amd64.deb ...
Unpacking gpgsm (2.4.4-2ubuntu17) ...
Selecting previously unselected package keyboxd.
Preparing to unpack .../173-keyboxd_2.4.4-2ubuntu17_amd64.deb ...
Unpacking keyboxd (2.4.4-2ubuntu17) ...
Selecting previously unselected package gnupg.
Preparing to unpack .../174-gnupg_2.4.4-2ubuntu17_all.deb ...
Unpacking gnupg (2.4.4-2ubuntu17) ...
Selecting previously unselected package libfile-dirlist-perl.
Preparing to unpack .../175-libfile-dirlist-perl_0.05-3_all.deb ...
Unpacking libfile-dirlist-perl (0.05-3) ...
Selecting previously unselected package libfile-which-perl.
Preparing to unpack .../176-libfile-which-perl_1.27-2_all.deb ...
Unpacking libfile-which-perl (1.27-2) ...
Selecting previously unselected package libfile-homedir-perl.
Preparing to unpack .../177-libfile-homedir-perl_1.006-2_all.deb ...
Unpacking libfile-homedir-perl (1.006-2) ...
Selecting previously unselected package libfile-touch-perl.
Preparing to unpack .../178-libfile-touch-perl_0.12-2_all.deb ...
Unpacking libfile-touch-perl (0.12-2) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../179-libio-pty-perl_1%3a1.20-1build2_amd64.deb ...
Unpacking libio-pty-perl (1:1.20-1build2) ...
Selecting previously unselected package libipc-run-perl.
Preparing to unpack .../180-libipc-run-perl_20231003.0-2_all.deb ...
Unpacking libipc-run-perl (20231003.0-2) ...
Selecting previously unselected package libclass-method-modifiers-perl.
Preparing to unpack .../181-libclass-method-modifiers-perl_2.15-1_all.deb ...
Unpacking libclass-method-modifiers-perl (2.15-1) ...
Selecting previously unselected package libclass-xsaccessor-perl.
Preparing to unpack .../182-libclass-xsaccessor-perl_1.19-4build4_amd64.deb ...
Unpacking libclass-xsaccessor-perl (1.19-4build4) ...
Selecting previously unselected package libb-hooks-op-check-perl:amd64.
Preparing to unpack .../183-libb-hooks-op-check-perl_0.22-3build1_amd64.deb ...
Unpacking libb-hooks-op-check-perl:amd64 (0.22-3build1) ...
Selecting previously unselected package libdynaloader-functions-perl.
Preparing to unpack .../184-libdynaloader-functions-perl_0.003-3_all.deb ...
Unpacking libdynaloader-functions-perl (0.003-3) ...
Selecting previously unselected package libdevel-callchecker-perl:amd64.
Preparing to unpack .../185-libdevel-callchecker-perl_0.009-1_amd64.deb ...
Unpacking libdevel-callchecker-perl:amd64 (0.009-1) ...
Selecting previously unselected package libparams-classify-perl:amd64.
Preparing to unpack .../186-libparams-classify-perl_0.015-2build5_amd64.deb ...
Unpacking libparams-classify-perl:amd64 (0.015-2build5) ...
Selecting previously unselected package libmodule-runtime-perl.
Preparing to unpack .../187-libmodule-runtime-perl_0.016-2_all.deb ...
Unpacking libmodule-runtime-perl (0.016-2) ...
Selecting previously unselected package libimport-into-perl.
Preparing to unpack .../188-libimport-into-perl_1.002005-2_all.deb ...
Unpacking libimport-into-perl (1.002005-2) ...
Selecting previously unselected package librole-tiny-perl.
Preparing to unpack .../189-librole-tiny-perl_2.002004-1_all.deb ...
Unpacking librole-tiny-perl (2.002004-1) ...
Selecting previously unselected package libsub-quote-perl.
Preparing to unpack .../190-libsub-quote-perl_2.006008-1ubuntu1_all.deb ...
Unpacking libsub-quote-perl (2.006008-1ubuntu1) ...
Selecting previously unselected package libmoo-perl.
Preparing to unpack .../191-libmoo-perl_2.005005-1_all.deb ...
Unpacking libmoo-perl (2.005005-1) ...
Selecting previously unselected package libencode-locale-perl.
Preparing to unpack .../192-libencode-locale-perl_1.05-3_all.deb ...
Unpacking libencode-locale-perl (1.05-3) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../193-libtimedate-perl_2.3300-2_all.deb ...
Unpacking libtimedate-perl (2.3300-2) ...
Selecting previously unselected package libhttp-date-perl.
Preparing to unpack .../194-libhttp-date-perl_6.06-1_all.deb ...
Unpacking libhttp-date-perl (6.06-1) ...
Selecting previously unselected package libfile-listing-perl.
Preparing to unpack .../195-libfile-listing-perl_6.16-1_all.deb ...
Unpacking libfile-listing-perl (6.16-1) ...
Selecting previously unselected package libhtml-tagset-perl.
Preparing to unpack .../196-libhtml-tagset-perl_3.24-1_all.deb ...
Unpacking libhtml-tagset-perl (3.24-1) ...
Selecting previously unselected package liburi-perl.
Preparing to unpack .../197-liburi-perl_5.28-1_all.deb ...
Unpacking liburi-perl (5.28-1) ...
Selecting previously unselected package libhtml-parser-perl:amd64.
Preparing to unpack .../198-libhtml-parser-perl_3.82-1_amd64.deb ...
Unpacking libhtml-parser-perl:amd64 (3.82-1) ...
Selecting previously unselected package libhtml-tree-perl.
Preparing to unpack .../199-libhtml-tree-perl_5.07-3_all.deb ...
Unpacking libhtml-tree-perl (5.07-3) ...
Selecting previously unselected package libclone-perl:amd64.
Preparing to unpack .../200-libclone-perl_0.46-1build3_amd64.deb ...
Unpacking libclone-perl:amd64 (0.46-1build3) ...
Selecting previously unselected package libio-html-perl.
Preparing to unpack .../201-libio-html-perl_1.004-3_all.deb ...
Unpacking libio-html-perl (1.004-3) ...
Selecting previously unselected package liblwp-mediatypes-perl.
Preparing to unpack .../202-liblwp-mediatypes-perl_6.04-2_all.deb ...
Unpacking liblwp-mediatypes-perl (6.04-2) ...
Selecting previously unselected package libhttp-message-perl.
Preparing to unpack .../203-libhttp-message-perl_6.45-1ubuntu1_all.deb ...
Unpacking libhttp-message-perl (6.45-1ubuntu1) ...
Selecting previously unselected package libhttp-cookies-perl.
Preparing to unpack .../204-libhttp-cookies-perl_6.11-1_all.deb ...
Unpacking libhttp-cookies-perl (6.11-1) ...
Selecting previously unselected package libhttp-negotiate-perl.
Preparing to unpack .../205-libhttp-negotiate-perl_6.01-2_all.deb ...
Unpacking libhttp-negotiate-perl (6.01-2) ...
Selecting previously unselected package perl-openssl-defaults:amd64.
Preparing to unpack .../206-perl-openssl-defaults_7build3_amd64.deb ...
Unpacking perl-openssl-defaults:amd64 (7build3) ...
Selecting previously unselected package libnet-ssleay-perl:amd64.
Preparing to unpack .../207-libnet-ssleay-perl_1.94-1build4_amd64.deb ...
Unpacking libnet-ssleay-perl:amd64 (1.94-1build4) ...
Selecting previously unselected package libio-socket-ssl-perl.
Preparing to unpack .../208-libio-socket-ssl-perl_2.085-1_all.deb ...
Unpacking libio-socket-ssl-perl (2.085-1) ...
Selecting previously unselected package libnet-http-perl.
Preparing to unpack .../209-libnet-http-perl_6.23-1_all.deb ...
Unpacking libnet-http-perl (6.23-1) ...
Selecting previously unselected package liblwp-protocol-https-perl.
Preparing to unpack .../210-liblwp-protocol-https-perl_6.14-1_all.deb ...
Unpacking liblwp-protocol-https-perl (6.14-1) ...
Selecting previously unselected package libtry-tiny-perl.
Preparing to unpack .../211-libtry-tiny-perl_0.31-2_all.deb ...
Unpacking libtry-tiny-perl (0.31-2) ...
Selecting previously unselected package libwww-robotrules-perl.
Preparing to unpack .../212-libwww-robotrules-perl_6.02-1_all.deb ...
Unpacking libwww-robotrules-perl (6.02-1) ...
Selecting previously unselected package libwww-perl.
Preparing to unpack .../213-libwww-perl_6.77-1_all.deb ...
Unpacking libwww-perl (6.77-1) ...
Selecting previously unselected package patchutils.
Preparing to unpack .../214-patchutils_0.4.2-1build3_amd64.deb ...
Unpacking patchutils (0.4.2-1build3) ...
Selecting previously unselected package wdiff.
Preparing to unpack .../215-wdiff_1.2.2-6build1_amd64.deb ...
Unpacking wdiff (1.2.2-6build1) ...
Selecting previously unselected package devscripts.
Preparing to unpack .../216-devscripts_2.23.7ubuntu1_all.deb ...
Unpacking devscripts (2.23.7ubuntu1) ...
Selecting previously unselected package fastjar.
Preparing to unpack .../217-fastjar_2%3a0.98-7_amd64.deb ...
Unpacking fastjar (2:0.98-7) ...
Selecting previously unselected package jarwrapper.
Preparing to unpack .../218-jarwrapper_0.79_all.deb ...
Unpacking jarwrapper (0.79) ...
Selecting previously unselected package unzip.
Preparing to unpack .../219-unzip_6.0-28ubuntu4_amd64.deb ...
Unpacking unzip (6.0-28ubuntu4) ...
Selecting previously unselected package java-wrappers.
Preparing to unpack .../220-java-wrappers_0.4_all.deb ...
Unpacking java-wrappers (0.4) ...
Selecting previously unselected package javahelper.
Preparing to unpack .../221-javahelper_0.79_all.deb ...
Unpacking javahelper (0.79) ...
Selecting previously unselected package libhamcrest-java.
Preparing to unpack .../222-libhamcrest-java_2.2-2_all.deb ...
Unpacking libhamcrest-java (2.2-2) ...
Selecting previously unselected package junit4.
Preparing to unpack .../223-junit4_4.13.2-4_all.deb ...
Unpacking junit4 (4.13.2-4) ...
Selecting previously unselected package libapiguardian-java.
Preparing to unpack .../224-libapiguardian-java_1.1.2-1_all.deb ...
Unpacking libapiguardian-java (1.1.2-1) ...
Selecting previously unselected package libopentest4j-java.
Preparing to unpack .../225-libopentest4j-java_1.2.0-4_all.deb ...
Unpacking libopentest4j-java (1.2.0-4) ...
Selecting previously unselected package libopentest4j-reporting-java.
Preparing to unpack .../226-libopentest4j-reporting-java_0.1.0-M1-2_all.deb ...
Unpacking libopentest4j-reporting-java (0.1.0-M1-2) ...
Selecting previously unselected package libpicocli-java.
Preparing to unpack .../227-libpicocli-java_4.6.2-2_all.deb ...
Unpacking libpicocli-java (4.6.2-2) ...
Selecting previously unselected package libunivocity-parsers-java.
Preparing to unpack .../228-libunivocity-parsers-java_2.9.1-1_all.deb ...
Unpacking libunivocity-parsers-java (2.9.1-1) ...
Selecting previously unselected package junit5.
Preparing to unpack .../229-junit5_5.10.1-1_all.deb ...
Unpacking junit5 (5.10.1-1) ...
Selecting previously unselected package libactivation-java.
Preparing to unpack .../230-libactivation-java_1.2.0-2_all.deb ...
Unpacking libactivation-java (1.2.0-2) ...
Selecting previously unselected package libapache-pom-java.
Preparing to unpack .../231-libapache-pom-java_29-2_all.deb ...
Unpacking libapache-pom-java (29-2) ...
Selecting previously unselected package libasm-java.
Preparing to unpack .../232-libasm-java_9.7-1_all.deb ...
Unpacking libasm-java (9.7-1) ...
Selecting previously unselected package libatinject-jsr330-api-java.
Preparing to unpack .../233-libatinject-jsr330-api-java_1.0+ds1-5_all.deb ...
Unpacking libatinject-jsr330-api-java (1.0+ds1-5) ...
Selecting previously unselected package libcommons-parent-java.
Preparing to unpack .../234-libcommons-parent-java_56-1_all.deb ...
Unpacking libcommons-parent-java (56-1) ...
Selecting previously unselected package libcommons-lang3-java.
Preparing to unpack .../235-libcommons-lang3-java_3.14.0-1_all.deb ...
Unpacking libcommons-lang3-java (3.14.0-1) ...
Selecting previously unselected package libfreemarker-java.
Preparing to unpack .../236-libfreemarker-java_2.3.32-2_all.deb ...
Unpacking libfreemarker-java (2.3.32-2) ...
Selecting previously unselected package libgoogle-gson-java.
Preparing to unpack .../237-libgoogle-gson-java_2.10.1-1_all.deb ...
Unpacking libgoogle-gson-java (2.10.1-1) ...
Selecting previously unselected package libjoptsimple-java.
Preparing to unpack .../238-libjoptsimple-java_5.0.4-4_all.deb ...
Unpacking libjoptsimple-java (5.0.4-4) ...
Selecting previously unselected package libcommons-codec-java.
Preparing to unpack .../239-libcommons-codec-java_1.16.0-1_all.deb ...
Unpacking libcommons-codec-java (1.16.0-1) ...
Selecting previously unselected package libcommons-logging-java.
Preparing to unpack .../240-libcommons-logging-java_1.3.0-1ubuntu1_all.deb ...
Unpacking libcommons-logging-java (1.3.0-1ubuntu1) ...
Selecting previously unselected package libhttpcore-java.
Preparing to unpack .../241-libhttpcore-java_4.4.16-1_all.deb ...
Unpacking libhttpcore-java (4.4.16-1) ...
Selecting previously unselected package libhttpclient-java.
Preparing to unpack .../242-libhttpclient-java_4.5.14-1_all.deb ...
Unpacking libhttpclient-java (4.5.14-1) ...
Selecting previously unselected package liblightcouch-java.
Preparing to unpack .../243-liblightcouch-java_0.2.0-1_all.deb ...
Unpacking liblightcouch-java (0.2.0-1) ...
Selecting previously unselected package libmongodb-java.
Preparing to unpack .../244-libmongodb-java_3.6.3-2_all.deb ...
Unpacking libmongodb-java (3.6.3-2) ...
Selecting previously unselected package libslf4j-java.
Preparing to unpack .../245-libslf4j-java_1.7.32-1_all.deb ...
Unpacking libslf4j-java (1.7.32-1) ...
Selecting previously unselected package liblog4j2-java.
Preparing to unpack .../246-liblog4j2-java_2.19.0-2_all.deb ...
Unpacking liblog4j2-java (2.19.0-2) ...
Selecting previously unselected package libbarclay-java.
Preparing to unpack .../247-libbarclay-java_5.0.0+dfsg-1_all.deb ...
Unpacking libbarclay-java (5.0.0+dfsg-1) ...
Selecting previously unselected package libjaxp1.3-java.
Preparing to unpack .../248-libjaxp1.3-java_1.3.05-6_all.deb ...
Unpacking libjaxp1.3-java (1.3.05-6) ...
Selecting previously unselected package libxml-commons-external-java.
Preparing to unpack .../249-libxml-commons-external-java_1.4.01-6_all.deb ...
Unpacking libxml-commons-external-java (1.4.01-6) ...
Selecting previously unselected package libcommons-io-java.
Preparing to unpack .../250-libcommons-io-java_2.16.1-1_all.deb ...
Unpacking libcommons-io-java (2.16.1-1) ...
Selecting previously unselected package libxmlgraphics-commons-java.
Preparing to unpack .../251-libxmlgraphics-commons-java_2.8-2_all.deb ...
Unpacking libxmlgraphics-commons-java (2.8-2) ...
Selecting previously unselected package libbatik-java.
Preparing to unpack .../252-libbatik-java_1.17+dfsg-1_all.deb ...
Unpacking libbatik-java (1.17+dfsg-1) ...
Selecting previously unselected package libblas3:amd64.
Preparing to unpack .../253-libblas3_3.12.0-3build1_amd64.deb ...
Unpacking libblas3:amd64 (3.12.0-3build1) ...
Selecting previously unselected package libbsh-java.
Preparing to unpack .../254-libbsh-java_2.0b4-20_all.deb ...
Unpacking libbsh-java (2.0b4-20) ...
Selecting previously unselected package libmaven-shared-utils-java.
Preparing to unpack .../255-libmaven-shared-utils-java_3.3.4-1_all.deb ...
Unpacking libmaven-shared-utils-java (3.3.4-1) ...
Selecting previously unselected package libcommons-cli-java.
Preparing to unpack .../256-libcommons-cli-java_1.6.0-1_all.deb ...
Unpacking libcommons-cli-java (1.6.0-1) ...
Selecting previously unselected package libgeronimo-annotation-1.3-spec-java.
Preparing to unpack .../257-libgeronimo-annotation-1.3-spec-java_1.3-1_all.deb ...
Unpacking libgeronimo-annotation-1.3-spec-java (1.3-1) ...
Selecting previously unselected package libaopalliance-java.
Preparing to unpack .../258-libaopalliance-java_20070526-7_all.deb ...
Unpacking libaopalliance-java (20070526-7) ...
Selecting previously unselected package liberror-prone-java.
Preparing to unpack .../259-liberror-prone-java_2.18.0-1_all.deb ...
Unpacking liberror-prone-java (2.18.0-1) ...
Selecting previously unselected package libjsr305-java.
Preparing to unpack .../260-libjsr305-java_0.1~+svn49-11_all.deb ...
Unpacking libjsr305-java (0.1~+svn49-11) ...
Selecting previously unselected package libguava-java.
Preparing to unpack .../261-libguava-java_32.0.1-1_all.deb ...
Unpacking libguava-java (32.0.1-1) ...
Selecting previously unselected package libguice-java.
Preparing to unpack .../262-libguice-java_4.2.3-2_all.deb ...
Unpacking libguice-java (4.2.3-2) ...
Selecting previously unselected package libmaven-parent-java.
Preparing to unpack .../263-libmaven-parent-java_35-1_all.deb ...
Unpacking libmaven-parent-java (35-1) ...
Selecting previously unselected package libplexus-utils2-java.
Preparing to unpack .../264-libplexus-utils2-java_3.4.2-1_all.deb ...
Unpacking libplexus-utils2-java (3.4.2-1) ...
Selecting previously unselected package libwagon-provider-api-java.
Preparing to unpack .../265-libwagon-provider-api-java_3.5.3-1_all.deb ...
Unpacking libwagon-provider-api-java (3.5.3-1) ...
Selecting previously unselected package libmaven-resolver-java.
Preparing to unpack .../266-libmaven-resolver-java_1.6.3-1_all.deb ...
Unpacking libmaven-resolver-java (1.6.3-1) ...
Selecting previously unselected package libplexus-cipher-java.
Preparing to unpack .../267-libplexus-cipher-java_2.0-1_all.deb ...
Unpacking libplexus-cipher-java (2.0-1) ...
Selecting previously unselected package libplexus-classworlds-java.
Preparing to unpack .../268-libplexus-classworlds-java_2.7.0-1_all.deb ...
Unpacking libplexus-classworlds-java (2.7.0-1) ...
Selecting previously unselected package libplexus-component-annotations-java.
Preparing to unpack .../269-libplexus-component-annotations-java_2.1.1-1_all.deb ...
Unpacking libplexus-component-annotations-java (2.1.1-1) ...
Selecting previously unselected package libplexus-interpolation-java.
Preparing to unpack .../270-libplexus-interpolation-java_1.26-1_all.deb ...
Unpacking libplexus-interpolation-java (1.26-1) ...
Selecting previously unselected package libplexus-sec-dispatcher-java.
Preparing to unpack .../271-libplexus-sec-dispatcher-java_2.0-3_all.deb ...
Unpacking libplexus-sec-dispatcher-java (2.0-3) ...
Selecting previously unselected package libgeronimo-interceptor-3.0-spec-java.
Preparing to unpack .../272-libgeronimo-interceptor-3.0-spec-java_1.0.1-4fakesync_all.deb ...
Unpacking libgeronimo-interceptor-3.0-spec-java (1.0.1-4fakesync) ...
Selecting previously unselected package libcdi-api-java.
Preparing to unpack .../273-libcdi-api-java_1.2-3_all.deb ...
Unpacking libcdi-api-java (1.2-3) ...
Selecting previously unselected package libsisu-inject-java.
Preparing to unpack .../274-libsisu-inject-java_0.3.4-2_all.deb ...
Unpacking libsisu-inject-java (0.3.4-2) ...
Selecting previously unselected package libsisu-plexus-java.
Preparing to unpack .../275-libsisu-plexus-java_0.3.4-3_all.deb ...
Unpacking libsisu-plexus-java (0.3.4-3) ...
Selecting previously unselected package libmaven3-core-java.
Preparing to unpack .../276-libmaven3-core-java_3.8.7-2_all.deb ...
Unpacking libmaven3-core-java (3.8.7-2) ...
Selecting previously unselected package libmaven-shared-io-java.
Preparing to unpack .../277-libmaven-shared-io-java_3.0.0-4_all.deb ...
Unpacking libmaven-shared-io-java (3.0.0-4) ...
Selecting previously unselected package libmaven-file-management-java.
Preparing to unpack .../278-libmaven-file-management-java_3.0.0-1_all.deb ...
Unpacking libmaven-file-management-java (3.0.0-1) ...
Selecting previously unselected package libbuild-helper-maven-plugin-java.
Preparing to unpack .../279-libbuild-helper-maven-plugin-java_3.3.0-1_all.deb ...
Unpacking libbuild-helper-maven-plugin-java (3.3.0-1) ...
Selecting previously unselected package libbyte-buddy-java.
Preparing to unpack .../280-libbyte-buddy-java_1.14.13-1_all.deb ...
Unpacking libbyte-buddy-java (1.14.13-1) ...
Selecting previously unselected package libcolt-free-java.
Preparing to unpack .../281-libcolt-free-java_1.2.0+dfsg-8_all.deb ...
Unpacking libcolt-free-java (1.2.0+dfsg-8) ...
Selecting previously unselected package libcommons-collections3-java.
Preparing to unpack .../282-libcommons-collections3-java_3.2.2-3_all.deb ...
Unpacking libcommons-collections3-java (3.2.2-3) ...
Selecting previously unselected package libcommons-beanutils-java.
Preparing to unpack .../283-libcommons-beanutils-java_1.9.4-2_all.deb ...
Unpacking libcommons-beanutils-java (1.9.4-2) ...
Selecting previously unselected package libcommons-collections4-java.
Preparing to unpack .../284-libcommons-collections4-java_4.4-2_all.deb ...
Unpacking libcommons-collections4-java (4.4-2) ...
Selecting previously unselected package libcommons-compress-java.
Preparing to unpack .../285-libcommons-compress-java_1.25.0-1_all.deb ...
Unpacking libcommons-compress-java (1.25.0-1) ...
Selecting previously unselected package libcommons-lang-java.
Preparing to unpack .../286-libcommons-lang-java_2.6-10_all.deb ...
Unpacking libcommons-lang-java (2.6-10) ...
Selecting previously unselected package libcommons-configuration-java.
Preparing to unpack .../287-libcommons-configuration-java_1.10-6_all.deb ...
Unpacking libcommons-configuration-java (1.10-6) ...
Selecting previously unselected package libcommons-digester-java.
Preparing to unpack .../288-libcommons-digester-java_1.8.1-6_all.deb ...
Unpacking libcommons-digester-java (1.8.1-6) ...
Selecting previously unselected package libcommons-exec-java.
Preparing to unpack .../289-libcommons-exec-java_1.3-2_all.deb ...
Unpacking libcommons-exec-java (1.3-2) ...
Selecting previously unselected package libcommons-jexl2-java.
Preparing to unpack .../290-libcommons-jexl2-java_2.1.1-6_all.deb ...
Unpacking libcommons-jexl2-java (2.1.1-6) ...
Selecting previously unselected package libcommons-math-java.
Preparing to unpack .../291-libcommons-math-java_2.2-8_all.deb ...
Unpacking libcommons-math-java (2.2-8) ...
Selecting previously unselected package libcommons-math3-java.
Preparing to unpack .../292-libcommons-math3-java_3.6.1-3_all.deb ...
Unpacking libcommons-math3-java (3.6.1-3) ...
Selecting previously unselected package libplexus-io-java.
Preparing to unpack .../293-libplexus-io-java_3.3.1-2_all.deb ...
Unpacking libplexus-io-java (3.3.1-2) ...
Selecting previously unselected package libsnappy1v5:amd64.
Preparing to unpack .../294-libsnappy1v5_1.2.0-2_amd64.deb ...
Unpacking libsnappy1v5:amd64 (1.2.0-2) ...
Selecting previously unselected package libsnappy-jni.
Preparing to unpack .../295-libsnappy-jni_1.1.10.5-2_amd64.deb ...
Unpacking libsnappy-jni (1.1.10.5-2) ...
Selecting previously unselected package libsnappy-java.
Preparing to unpack .../296-libsnappy-java_1.1.10.5-2_all.deb ...
Unpacking libsnappy-java (1.1.10.5-2) ...
Selecting previously unselected package libxz-java.
Preparing to unpack .../297-libxz-java_1.9-1_all.deb ...
Unpacking libxz-java (1.9-1) ...
Selecting previously unselected package libplexus-archiver-java.
Preparing to unpack .../298-libplexus-archiver-java_4.6.1-1_all.deb ...
Unpacking libplexus-archiver-java (4.6.1-1) ...
Selecting previously unselected package libmaven-archiver-java.
Preparing to unpack .../299-libmaven-archiver-java_3.6.0-1_all.deb ...
Unpacking libmaven-archiver-java (3.6.0-1) ...
Selecting previously unselected package libmaven-jar-plugin-java.
Preparing to unpack .../300-libmaven-jar-plugin-java_3.3.0-2_all.deb ...
Unpacking libmaven-jar-plugin-java (3.3.0-2) ...
Selecting previously unselected package libcommons-text-java.
Preparing to unpack .../301-libcommons-text-java_1.11.0-1_all.deb ...
Unpacking libcommons-text-java (1.11.0-1) ...
Selecting previously unselected package libcommons-validator-java.
Preparing to unpack .../302-libcommons-validator-java_1%3a1.7-1_all.deb ...
Unpacking libcommons-validator-java (1:1.7-1) ...
Selecting previously unselected package librtmp1:amd64.
Preparing to unpack .../303-librtmp1_2.4+20151223.gitfa8646d.1-2build7_amd64.deb ...
Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build7) ...
Selecting previously unselected package libssh-4:amd64.
Preparing to unpack .../304-libssh-4_0.10.6-2build2_amd64.deb ...
Unpacking libssh-4:amd64 (0.10.6-2build2) ...
Selecting previously unselected package libcurl4t64:amd64.
Preparing to unpack .../305-libcurl4t64_8.5.0-2ubuntu10.1_amd64.deb ...
Unpacking libcurl4t64:amd64 (8.5.0-2ubuntu10.1) ...
Selecting previously unselected package libdistlib-java.
Preparing to unpack .../306-libdistlib-java_1.0-4_all.deb ...
Unpacking libdistlib-java (1.0-4) ...
Selecting previously unselected package libjaxen-java.
Preparing to unpack .../307-libjaxen-java_1.1.6-4_all.deb ...
Unpacking libjaxen-java (1.1.6-4) ...
Selecting previously unselected package libdom4j-java.
Preparing to unpack .../308-libdom4j-java_2.1.4-1_all.deb ...
Unpacking libdom4j-java (2.1.4-1) ...
Selecting previously unselected package libdoxia-core-java.
Preparing to unpack .../309-libdoxia-core-java_1.12.0-1_all.deb ...
Unpacking libdoxia-core-java (1.12.0-1) ...
Selecting previously unselected package libfontbox2-java.
Preparing to unpack .../310-libfontbox2-java_2.0.29-1_all.deb ...
Unpacking libfontbox2-java (2.0.29-1) ...
Selecting previously unselected package libqdox-java.
Preparing to unpack .../311-libqdox-java_1.12.1-3_all.deb ...
Unpacking libqdox-java (1.12.1-3) ...
Selecting previously unselected package libfop-java.
Preparing to unpack .../312-libfop-java_1%3a2.8-3_all.deb ...
Unpacking libfop-java (1:2.8-3) ...
Selecting previously unselected package libitext1-java.
Preparing to unpack .../313-libitext1-java_1.4-7_all.deb ...
Unpacking libitext1-java (1.4-7) ...
Selecting previously unselected package libxbean-reflect-java.
Preparing to unpack .../314-libxbean-reflect-java_4.5-8_all.deb ...
Unpacking libxbean-reflect-java (4.5-8) ...
Selecting previously unselected package libplexus-container-default-java.
Preparing to unpack .../315-libplexus-container-default-java_2.1.1-1_all.deb ...
Unpacking libplexus-container-default-java (2.1.1-1) ...
Selecting previously unselected package libdoxia-java.
Preparing to unpack .../316-libdoxia-java_1.12.0-1_all.deb ...
Unpacking libdoxia-java (1.12.0-1) ...
Selecting previously unselected package libmaven-reporting-api-java.
Preparing to unpack .../317-libmaven-reporting-api-java_3.1.1-1_all.deb ...
Unpacking libmaven-reporting-api-java (3.1.1-1) ...
Selecting previously unselected package libplexus-i18n-java.
Preparing to unpack .../318-libplexus-i18n-java_1.0-beta-10-6_all.deb ...
Unpacking libplexus-i18n-java (1.0-beta-10-6) ...
Selecting previously unselected package velocity.
Preparing to unpack .../319-velocity_1.7-7_all.deb ...
Unpacking velocity (1.7-7) ...
Selecting previously unselected package libplexus-velocity-java.
Preparing to unpack .../320-libplexus-velocity-java_1.2-3.1_all.deb ...
Unpacking libplexus-velocity-java (1.2-3.1) ...
Selecting previously unselected package liboro-java.
Preparing to unpack .../321-liboro-java_2.0.8a-14_all.deb ...
Unpacking liboro-java (2.0.8a-14) ...
Selecting previously unselected package libvelocity-tools-java.
Preparing to unpack .../322-libvelocity-tools-java_2.0-9_all.deb ...
Unpacking libvelocity-tools-java (2.0-9) ...
Selecting previously unselected package libxml-commons-resolver1.1-java.
Preparing to unpack .../323-libxml-commons-resolver1.1-java_1.2-11_all.deb ...
Unpacking libxml-commons-resolver1.1-java (1.2-11) ...
Selecting previously unselected package libxerces2-java.
Preparing to unpack .../324-libxerces2-java_2.12.2-1_all.deb ...
Unpacking libxerces2-java (2.12.2-1) ...
Selecting previously unselected package libxalan2-java.
Preparing to unpack .../325-libxalan2-java_2.7.2-4_all.deb ...
Unpacking libxalan2-java (2.7.2-4) ...
Selecting previously unselected package libdoxia-sitetools-java.
Preparing to unpack .../326-libdoxia-sitetools-java_1.11.1-1_all.deb ...
Unpacking libdoxia-sitetools-java (1.11.1-1) ...
Selecting previously unselected package libfastutil-java.
Preparing to unpack .../327-libfastutil-java_8.5.12+dfsg-2_all.deb ...
Unpacking libfastutil-java (8.5.12+dfsg-2) ...
Selecting previously unselected package libxpp3-java.
Preparing to unpack .../328-libxpp3-java_1.1.4c-3_all.deb ...
Unpacking libxpp3-java (1.1.4c-3) ...
Selecting previously unselected package libxstream-java.
Preparing to unpack .../329-libxstream-java_1.4.20-1_all.deb ...
Unpacking libxstream-java (1.4.20-1) ...
Selecting previously unselected package libjsap-java.
Preparing to unpack .../330-libjsap-java_2.1-5_all.deb ...
Unpacking libjsap-java (2.1-5) ...
Selecting previously unselected package liblogback-java.
Preparing to unpack .../331-liblogback-java_1%3a1.2.11-5_all.deb ...
Unpacking liblogback-java (1:1.2.11-5) ...
Selecting previously unselected package libdsiutils-java.
Preparing to unpack .../332-libdsiutils-java_2.7.3+dfsg-1_all.deb ...
Unpacking libdsiutils-java (2.7.3+dfsg-1) ...
Selecting previously unselected package libobjenesis-java.
Preparing to unpack .../333-libobjenesis-java_3.3-3_all.deb ...
Unpacking libobjenesis-java (3.3-3) ...
Selecting previously unselected package libeasymock-java.
Preparing to unpack .../334-libeasymock-java_5.2.0-1_all.deb ...
Unpacking libeasymock-java (5.2.0-1) ...
Selecting previously unselected package libel-api-java.
Preparing to unpack .../335-libel-api-java_3.0.0-3_all.deb ...
Unpacking libel-api-java (3.0.0-3) ...
Selecting previously unselected package libexec-maven-plugin-java.
Preparing to unpack .../336-libexec-maven-plugin-java_3.1.0-2_all.deb ...
Unpacking libexec-maven-plugin-java (3.1.0-2) ...
Selecting previously unselected package libgatk-native-bindings-java.
Preparing to unpack .../337-libgatk-native-bindings-java_1.0.0+dfsg-2_all.deb ...
Unpacking libgatk-native-bindings-java (1.0.0+dfsg-2) ...
Selecting previously unselected package libgfortran5:amd64.
Preparing to unpack .../338-libgfortran5_14-20240429-1ubuntu1_amd64.deb ...
Unpacking libgfortran5:amd64 (14-20240429-1ubuntu1) ...
Selecting previously unselected package libmjson-java.
Preparing to unpack .../339-libmjson-java_1.4.0-3_all.deb ...
Unpacking libmjson-java (1.4.0-3) ...
Selecting previously unselected package libmbedcrypto7t64:amd64.
Preparing to unpack .../340-libmbedcrypto7t64_2.28.8-1_amd64.deb ...
Unpacking libmbedcrypto7t64:amd64 (2.28.8-1) ...
Selecting previously unselected package libmbedx509-1t64:amd64.
Preparing to unpack .../341-libmbedx509-1t64_2.28.8-1_amd64.deb ...
Unpacking libmbedx509-1t64:amd64 (2.28.8-1) ...
Selecting previously unselected package libmbedtls14t64:amd64.
Preparing to unpack .../342-libmbedtls14t64_2.28.8-1_amd64.deb ...
Unpacking libmbedtls14t64:amd64 (2.28.8-1) ...
Selecting previously unselected package ncbi-vdb-data.
Preparing to unpack .../343-ncbi-vdb-data_3.0.2+dfsg-2build2_all.deb ...
Unpacking ncbi-vdb-data (3.0.2+dfsg-2build2) ...
Selecting previously unselected package libncbi-vdb3:amd64.
Preparing to unpack .../344-libncbi-vdb3_3.0.2+dfsg-2build2_amd64.deb ...
Unpacking libncbi-vdb3:amd64 (3.0.2+dfsg-2build2) ...
Selecting previously unselected package libncbi-ngs3:amd64.
Preparing to unpack .../345-libncbi-ngs3_3.0.3+dfsg-6ubuntu5_amd64.deb ...
Unpacking libncbi-ngs3:amd64 (3.0.3+dfsg-6ubuntu5) ...
Selecting previously unselected package libngs-jni:amd64.
Preparing to unpack .../346-libngs-jni_3.0.3+dfsg-6ubuntu5_amd64.deb ...
Unpacking libngs-jni:amd64 (3.0.3+dfsg-6ubuntu5) ...
Selecting previously unselected package libngs-java:amd64.
Preparing to unpack .../347-libngs-java_3.0.3+dfsg-6ubuntu5_amd64.deb ...
Unpacking libngs-java:amd64 (3.0.3+dfsg-6ubuntu5) ...
Selecting previously unselected package librhino-java.
Preparing to unpack .../348-librhino-java_1.7.14-2.1_all.deb ...
Unpacking librhino-java (1.7.14-2.1) ...
Selecting previously unselected package libhtsjdk-java.
Preparing to unpack .../349-libhtsjdk-java_4.1.0+dfsg-1_all.deb ...
Unpacking libhtsjdk-java (4.1.0+dfsg-1) ...
Selecting previously unselected package libgkl-java.
Preparing to unpack .../350-libgkl-java_0.8.11+dfsg-2build1_all.deb ...
Unpacking libgkl-java (0.8.11+dfsg-2build1) ...
Selecting previously unselected package libicu4j-java.
Preparing to unpack .../351-libicu4j-java_73.2-1_all.deb ...
Unpacking libicu4j-java (73.2-1) ...
Selecting previously unselected package liblog4j1.2-java.
Preparing to unpack .../352-liblog4j1.2-java_1.2.17-11_all.deb ...
Unpacking liblog4j1.2-java (1.2.17-11) ...
Selecting previously unselected package libicb-utils-java.
Preparing to unpack .../353-libicb-utils-java_2.0.1+git20161002.afee1d9-5_all.deb ...
Unpacking libicb-utils-java (2.0.1+git20161002.afee1d9-5) ...
Selecting previously unselected package libice6:amd64.
Preparing to unpack .../354-libice6_2%3a1.0.10-1build3_amd64.deb ...
Unpacking libice6:amd64 (2:1.0.10-1build3) ...
Selecting previously unselected package libjansi-java.
Preparing to unpack .../355-libjansi-java_2.4.1-2_all.deb ...
Unpacking libjansi-java (2.4.1-2) ...
Selecting previously unselected package libjavassist-java.
Preparing to unpack .../356-libjavassist-java_1%3a3.27.0-1_all.deb ...
Unpacking libjavassist-java (1:3.27.0-1) ...
Selecting previously unselected package libjaxb-api-java.
Preparing to unpack .../357-libjaxb-api-java_2.3.1-1_all.deb ...
Unpacking libjaxb-api-java (2.3.1-1) ...
Selecting previously unselected package libjboss-logging-java.
Preparing to unpack .../358-libjboss-logging-java_3.5.3-1_all.deb ...
Unpacking libjboss-logging-java (3.5.3-1) ...
Selecting previously unselected package libjboss-vfs-java.
Preparing to unpack .../359-libjboss-vfs-java_3.2.15.Final-3_all.deb ...
Unpacking libjboss-vfs-java (3.2.15.Final-3) ...
Selecting previously unselected package libjcommander-java.
Preparing to unpack .../360-libjcommander-java_1.71-4_all.deb ...
Unpacking libjcommander-java (1.71-4) ...
Selecting previously unselected package libjsp-api-java.
Preparing to unpack .../361-libjsp-api-java_2.3.4-3_all.deb ...
Unpacking libjsp-api-java (2.3.4-3) ...
Selecting previously unselected package libservlet-api-java.
Preparing to unpack .../362-libservlet-api-java_4.0.1-2_all.deb ...
Unpacking libservlet-api-java (4.0.1-2) ...
Selecting previously unselected package libwebsocket-api-java.
Preparing to unpack .../363-libwebsocket-api-java_1.1-2_all.deb ...
Unpacking libwebsocket-api-java (1.1-2) ...
Selecting previously unselected package libjetty9-java.
Preparing to unpack .../364-libjetty9-java_9.4.54-1_all.deb ...
Unpacking libjetty9-java (9.4.54-1) ...
Selecting previously unselected package libjsoup-java.
Preparing to unpack .../365-libjsoup-java_1.15.3-1_all.deb ...
Unpacking libjsoup-java (1.15.3-1) ...
Selecting previously unselected package libjtidy-java.
Preparing to unpack .../366-libjtidy-java_7+svn20110807-5_all.deb ...
Unpacking libjtidy-java (7+svn20110807-5) ...
Selecting previously unselected package liblapack3:amd64.
Preparing to unpack .../367-liblapack3_3.12.0-3build1_amd64.deb ...
Unpacking liblapack3:amd64 (3.12.0-3build1) ...
Selecting previously unselected package libmaven-antrun-plugin-java.
Preparing to unpack .../368-libmaven-antrun-plugin-java_3.1.0-1_all.deb ...
Unpacking libmaven-antrun-plugin-java (3.1.0-1) ...
Selecting previously unselected package libmaven-common-artifact-filters-java.
Preparing to unpack .../369-libmaven-common-artifact-filters-java_3.3.2-1_all.deb ...
Unpacking libmaven-common-artifact-filters-java (3.3.2-1) ...
Selecting previously unselected package libmaven-artifact-transfer-java.
Preparing to unpack .../370-libmaven-artifact-transfer-java_0.13.1-2_all.deb ...
Unpacking libmaven-artifact-transfer-java (0.13.1-2) ...
Selecting previously unselected package libplexus-build-api-java.
Preparing to unpack .../371-libplexus-build-api-java_0.0.7-4_all.deb ...
Unpacking libplexus-build-api-java (0.0.7-4) ...
Selecting previously unselected package libmaven-filtering-java.
Preparing to unpack .../372-libmaven-filtering-java_3.3.0-1_all.deb ...
Unpacking libmaven-filtering-java (3.3.0-1) ...
Selecting previously unselected package libmaven-assembly-plugin-java.
Preparing to unpack .../373-libmaven-assembly-plugin-java_3.4.2-1_all.deb ...
Unpacking libmaven-assembly-plugin-java (3.4.2-1) ...
Selecting previously unselected package libmaven-clean-plugin-java.
Preparing to unpack .../374-libmaven-clean-plugin-java_3.2.0-2_all.deb ...
Unpacking libmaven-clean-plugin-java (3.2.0-2) ...
Selecting previously unselected package libmaven-shared-incremental-java.
Preparing to unpack .../375-libmaven-shared-incremental-java_1.1-4_all.deb ...
Unpacking libmaven-shared-incremental-java (1.1-4) ...
Selecting previously unselected package libplexus-compiler-java.
Preparing to unpack .../376-libplexus-compiler-java_2.12.1-2_all.deb ...
Unpacking libplexus-compiler-java (2.12.1-2) ...
Selecting previously unselected package libqdox2-java.
Preparing to unpack .../377-libqdox2-java_2.0.3-1_all.deb ...
Unpacking libqdox2-java (2.0.3-1) ...
Selecting previously unselected package libplexus-languages-java.
Preparing to unpack .../378-libplexus-languages-java_1.1.1-2_all.deb ...
Unpacking libplexus-languages-java (1.1.1-2) ...
Selecting previously unselected package libmaven-compiler-plugin-java.
Preparing to unpack .../379-libmaven-compiler-plugin-java_3.10.1-2_all.deb ...
Unpacking libmaven-compiler-plugin-java (3.10.1-2) ...
Selecting previously unselected package libmaven-dependency-analyzer-java.
Preparing to unpack .../380-libmaven-dependency-analyzer-java_1.13.0-1_all.deb ...
Unpacking libmaven-dependency-analyzer-java (1.13.0-1) ...
Selecting previously unselected package libmaven-dependency-tree-java.
Preparing to unpack .../381-libmaven-dependency-tree-java_3.2.1-1_all.deb ...
Unpacking libmaven-dependency-tree-java (3.2.1-1) ...
Selecting previously unselected package libmaven-reporting-impl-java.
Preparing to unpack .../382-libmaven-reporting-impl-java_3.2.0-2_all.deb ...
Unpacking libmaven-reporting-impl-java (3.2.0-2) ...
Selecting previously unselected package libmaven-dependency-plugin-java.
Preparing to unpack .../383-libmaven-dependency-plugin-java_3.5.0-1_all.deb ...
Unpacking libmaven-dependency-plugin-java (3.5.0-1) ...
Selecting previously unselected package libmaven-invoker-java.
Preparing to unpack .../384-libmaven-invoker-java_3.2.0-1_all.deb ...
Unpacking libmaven-invoker-java (3.2.0-1) ...
Selecting previously unselected package libplexus-interactivity-api-java.
Preparing to unpack .../385-libplexus-interactivity-api-java_1.1-2_all.deb ...
Unpacking libplexus-interactivity-api-java (1.1-2) ...
Selecting previously unselected package libmaven-javadoc-plugin-java.
Preparing to unpack .../386-libmaven-javadoc-plugin-java_3.4.1-3_all.deb ...
Unpacking libmaven-javadoc-plugin-java (3.4.1-3) ...
Selecting previously unselected package libplexus-container-default1.5-java.
Preparing to unpack .../387-libplexus-container-default1.5-java_2.1.1-1_all.deb ...
Unpacking libplexus-container-default1.5-java (2.1.1-1) ...
Selecting previously unselected package libplexus-ant-factory-java.
Preparing to unpack .../388-libplexus-ant-factory-java_1.0~alpha2.1-4_all.deb ...
Unpacking libplexus-ant-factory-java (1.0~alpha2.1-4) ...
Selecting previously unselected package libplexus-bsh-factory-java.
Preparing to unpack .../389-libplexus-bsh-factory-java_1.0~alpha7-5_all.deb ...
Unpacking libplexus-bsh-factory-java (1.0~alpha7-5) ...
Selecting previously unselected package libmaven-plugin-tools-java.
Preparing to unpack .../390-libmaven-plugin-tools-java_3.7.1-1_all.deb ...
Unpacking libmaven-plugin-tools-java (3.7.1-1) ...
Selecting previously unselected package libmaven-reporting-exec-java.
Preparing to unpack .../391-libmaven-reporting-exec-java_1.6.0-1_all.deb ...
Unpacking libmaven-reporting-exec-java (1.6.0-1) ...
Selecting previously unselected package libmaven-resources-plugin-java.
Preparing to unpack .../392-libmaven-resources-plugin-java_3.3.0-1_all.deb ...
Unpacking libmaven-resources-plugin-java (3.3.0-1) ...
Selecting previously unselected package libmaven-site-plugin-java.
Preparing to unpack .../393-libmaven-site-plugin-java_3.12.1-2_all.deb ...
Unpacking libmaven-site-plugin-java (3.12.1-2) ...
Selecting previously unselected package libmaven-source-plugin-java.
Preparing to unpack .../394-libmaven-source-plugin-java_3.2.1-2_all.deb ...
Unpacking libmaven-source-plugin-java (3.2.1-2) ...
Selecting previously unselected package libpaper1:amd64.
Preparing to unpack .../395-libpaper1_1.1.29build1_amd64.deb ...
Unpacking libpaper1:amd64 (1.1.29build1) ...
Selecting previously unselected package libpaper-utils.
Preparing to unpack .../396-libpaper-utils_1.1.29build1_amd64.deb ...
Unpacking libpaper-utils (1.1.29build1) ...
Selecting previously unselected package libpicard-java.
Preparing to unpack .../397-libpicard-java_3.1.1+dfsg-1_all.deb ...
Unpacking libpicard-java (3.1.1+dfsg-1) ...
Selecting previously unselected package libpj-java.
Preparing to unpack .../398-libpj-java_0.0~20150107+dfsg-5_all.deb ...
Unpacking libpj-java (0.0~20150107+dfsg-5) ...
Selecting previously unselected package libpkgconf3:amd64.
Preparing to unpack .../399-libpkgconf3_1.8.1-2build1_amd64.deb ...
Unpacking libpkgconf3:amd64 (1.8.1-2build1) ...
Selecting previously unselected package libprotobuf-lite32t64:amd64.
Preparing to unpack .../400-libprotobuf-lite32t64_3.21.12-8.2build1_amd64.deb ...
Unpacking libprotobuf-lite32t64:amd64 (3.21.12-8.2build1) ...
Selecting previously unselected package libprotobuf32t64:amd64.
Preparing to unpack .../401-libprotobuf32t64_3.21.12-8.2build1_amd64.deb ...
Unpacking libprotobuf32t64:amd64 (3.21.12-8.2build1) ...
Selecting previously unselected package libprotoc32t64:amd64.
Preparing to unpack .../402-libprotoc32t64_3.21.12-8.2build1_amd64.deb ...
Unpacking libprotoc32t64:amd64 (3.21.12-8.2build1) ...
Selecting previously unselected package libreflections-java.
Preparing to unpack .../403-libreflections-java_0.10.2+dfsg-2_all.deb ...
Unpacking libreflections-java (0.10.2+dfsg-2) ...
Selecting previously unselected package libsm6:amd64.
Preparing to unpack .../404-libsm6_2%3a1.2.3-1build3_amd64.deb ...
Unpacking libsm6:amd64 (2:1.2.3-1build3) ...
Selecting previously unselected package libsurefire-java.
Preparing to unpack .../405-libsurefire-java_2.22.3-2_all.deb ...
Unpacking libsurefire-java (2.22.3-2) ...
Selecting previously unselected package libtcl8.6:amd64.
Preparing to unpack .../406-libtcl8.6_8.6.14+dfsg-1build1_amd64.deb ...
Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1build1) ...
Selecting previously unselected package libxft2:amd64.
Preparing to unpack .../407-libxft2_2.3.6-1build1_amd64.deb ...
Unpacking libxft2:amd64 (2.3.6-1build1) ...
Selecting previously unselected package libxss1:amd64.
Preparing to unpack .../408-libxss1_1%3a1.2.3-1build3_amd64.deb ...
Unpacking libxss1:amd64 (1:1.2.3-1build3) ...
Selecting previously unselected package libtk8.6:amd64.
Preparing to unpack .../409-libtk8.6_8.6.14-1build1_amd64.deb ...
Unpacking libtk8.6:amd64 (8.6.14-1build1) ...
Selecting previously unselected package libwagon-file-java.
Preparing to unpack .../410-libwagon-file-java_3.5.3-1_all.deb ...
Unpacking libwagon-file-java (3.5.3-1) ...
Selecting previously unselected package libwagon-http-shaded-java.
Preparing to unpack .../411-libwagon-http-shaded-java_3.5.3-1_all.deb ...
Unpacking libwagon-http-shaded-java (3.5.3-1) ...
Selecting previously unselected package libxml2-utils.
Preparing to unpack .../412-libxml2-utils_2.9.14+dfsg-1.3ubuntu3_amd64.deb ...
Unpacking libxml2-utils (2.9.14+dfsg-1.3ubuntu3) ...
Selecting previously unselected package libxt6t64:amd64.
Preparing to unpack .../413-libxt6t64_1%3a1.2.1-1.2build1_amd64.deb ...
Unpacking libxt6t64:amd64 (1:1.2.1-1.2build1) ...
Selecting previously unselected package maven.
Preparing to unpack .../414-maven_3.8.7-2_all.deb ...
Unpacking maven (3.8.7-2) ...
Selecting previously unselected package maven-repo-helper.
Preparing to unpack .../415-maven-repo-helper_1.11_all.deb ...
Unpacking maven-repo-helper (1.11) ...
Selecting previously unselected package maven-debian-helper.
Preparing to unpack .../416-maven-debian-helper_2.6.4_all.deb ...
Unpacking maven-debian-helper (2.6.4) ...
Selecting previously unselected package pkgconf-bin.
Preparing to unpack .../417-pkgconf-bin_1.8.1-2build1_amd64.deb ...
Unpacking pkgconf-bin (1.8.1-2build1) ...
Selecting previously unselected package pkgconf:amd64.
Preparing to unpack .../418-pkgconf_1.8.1-2build1_amd64.deb ...
Unpacking pkgconf:amd64 (1.8.1-2build1) ...
Selecting previously unselected package zip.
Preparing to unpack .../419-zip_3.0-13build1_amd64.deb ...
Unpacking zip (3.0-13build1) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../420-xdg-utils_1.1.3-4.1ubuntu3_all.deb ...
Unpacking xdg-utils (1.1.3-4.1ubuntu3) ...
Selecting previously unselected package r-base-core.
Preparing to unpack .../421-r-base-core_4.4.0-2_amd64.deb ...
Unpacking r-base-core (4.4.0-2) ...
Selecting previously unselected package r-cran-rjava.
Preparing to unpack .../422-r-cran-rjava_1.0-11-1_amd64.deb ...
Unpacking r-cran-rjava (1.0-11-1) ...
Selecting previously unselected package testng.
Preparing to unpack .../423-testng_6.9.12-4_all.deb ...
Unpacking testng (6.9.12-4) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../424-zlib1g-dev_1%3a1.3.dfsg-3.1ubuntu2_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.3.dfsg-3.1ubuntu2) ...
Selecting previously unselected package ant-contrib.
Preparing to unpack .../425-ant-contrib_1.0~b3+svn177-12_all.deb ...
Unpacking ant-contrib (1.0~b3+svn177-12) ...
Selecting previously unselected package libjbzip2-java.
Preparing to unpack .../426-libjbzip2-java_0.9.1-8_all.deb ...
Unpacking libjbzip2-java (0.9.1-8) ...
Selecting previously unselected package libprotobuf-dev:amd64.
Preparing to unpack .../427-libprotobuf-dev_3.21.12-8.2build1_amd64.deb ...
Unpacking libprotobuf-dev:amd64 (3.21.12-8.2build1) ...
Selecting previously unselected package libprotobuf-java.
Preparing to unpack .../428-libprotobuf-java_3.21.12-8.2build1_all.deb ...
Unpacking libprotobuf-java (3.21.12-8.2build1) ...
Selecting previously unselected package protobuf-compiler.
Preparing to unpack .../429-protobuf-compiler_3.21.12-8.2build1_amd64.deb ...
Unpacking protobuf-compiler (3.21.12-8.2build1) ...
Selecting previously unselected package sbuild-build-depends-main-dummy.
Preparing to unpack .../430-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ...
Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libprotobuf-lite32t64:amd64 (3.21.12-8.2build1) ...
Setting up libksba8:amd64 (1.6.6-1build1) ...
Setting up media-types (10.1.0) ...
Setting up libpipeline1:amd64 (1.5.7-2) ...
Setting up fastjar (2:0.98-7) ...
Setting up libgraphite2-3:amd64 (1.3.14-2build1) ...
Setting up liblcms2-2:amd64 (2.14-2build1) ...
Setting up libpixman-1-0:amd64 (0.42.2-1build1) ...
Setting up libjcommander-java (1.71-4) ...
Setting up libfastutil-java (8.5.12+dfsg-2) ...
Setting up wdiff (1.2.2-6build1) ...
Setting up libsharpyuv0:amd64 (1.4.0-0.1) ...
Setting up libpciaccess0:amd64 (0.17-3build1) ...
Setting up libslf4j-java (1.7.32-1) ...
Setting up libprotobuf32t64:amd64 (3.21.12-8.2build1) ...
Setting up libfile-which-perl (1.27-2) ...
Setting up libxau6:amd64 (1:1.0.9-1build6) ...
Setting up libplexus-utils2-java (3.4.2-1) ...
Setting up libplexus-classworlds-java (2.7.0-1) ...
Setting up libqdox-java (1.12.1-3) ...
Setting up libopentest4j-reporting-java (0.1.0-M1-2) ...
Setting up libplexus-build-api-java (0.0.7-4) ...
Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu2) ...
Setting up libjsr305-java (0.1~+svn49-11) ...
Setting up hicolor-icon-theme (0.17-2) ...
Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ...
Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ...
Setting up libicu4j-java (73.2-1) ...
Setting up java-common (0.75+exp1) ...
Setting up libdynaloader-functions-perl (0.003-3) ...
Setting up libdatrie1:amd64 (0.2.13-3build1) ...
Setting up libobjenesis-java (3.3-3) ...
Setting up libclass-method-modifiers-perl (2.15-1) ...
Setting up libqdox2-java (2.0.3-1) ...
Setting up libaopalliance-java (20070526-7) ...
Setting up libcommons-cli-java (1.6.0-1) ...
Setting up libio-pty-perl (1:1.20-1build2) ...
Setting up libmagic-mgc (1:5.45-3build1) ...
Setting up libcommons-exec-java (1.3-2) ...
Setting up liblogback-java (1:1.2.11-5) ...
Setting up libclone-perl:amd64 (0.46-1build3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglvnd0:amd64 (1.7.0-1build1) ...
Setting up libgoogle-gson-java (2.10.1-1) ...
Setting up libmjson-java (1.4.0-3) ...
Setting up libhtml-tagset-perl (3.24-1) ...
Setting up unzip (6.0-28ubuntu4) ...
Setting up libdebhelper-perl (13.14.1ubuntu5) ...
Setting up libbrotli1:amd64 (1.1.0-2build2) ...
Setting up gpgsm (2.4.4-2ubuntu17) ...
Setting up liblwp-mediatypes-perl (6.04-2) ...
Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3ubuntu3) ...
Setting up libmagic1t64:amd64 (1:5.45-3build1) ...
Setting up libpicocli-java (4.6.2-2) ...
Setting up libasm-java (9.7-1) ...
Setting up x11-common (1:7.7+23ubuntu3) ...
Running in chroot, ignoring request.
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libtry-tiny-perl (0.31-2) ...
Setting up libsensors-config (1:3.6.0-9build1) ...
Setting up libpsl5t64:amd64 (0.21.2-1.1build1) ...
Setting up libnghttp2-14:amd64 (1.61.0-1) ...
Setting up libdeflate0:amd64 (1.20-1) ...
Setting up perl-openssl-defaults:amd64 (7build3) ...
Setting up liblog4j1.2-java (1.2.17-11) ...
Setting up gettext-base (0.21-14ubuntu2) ...
Setting up m4 (1.4.19-4build1) ...
Setting up libel-api-java (3.0.0-3) ...
Setting up xkb-data (2.41-2ubuntu1) ...
Setting up libencode-locale-perl (1.05-3) ...
Setting up libplexus-component-annotations-java (2.1.1-1) ...
Setting up file (1:5.45-3build1) ...
Setting up libjboss-logging-java (3.5.3-1) ...
Setting up libunivocity-parsers-java (2.9.1-1) ...
Setting up libjbig0:amd64 (2.1-6.1ubuntu2) ...
Setting up libelf1t64:amd64 (0.191-1) ...
Setting up liboro-java (2.0.8a-14) ...
Setting up libsnappy1v5:amd64 (1.2.0-2) ...
Setting up libexec-maven-plugin-java (3.1.0-2) ...
Setting up libdw1t64:amd64 (0.191-1) ...
Setting up libfontbox2-java (2.0.29-1) ...
Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-5ubuntu3) ...
Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ...
Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4fakesync) ...
Setting up libcommons-collections3-java (3.2.2-3) ...
Setting up libasound2-data (1.2.11-1build2) ...
Setting up patchutils (0.4.2-1build3) ...
Setting up libjavassist-java (1:3.27.0-1) ...
Setting up zip (3.0-13build1) ...
Setting up librhino-java (1.7.14-2.1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libglib2.0-0t64:amd64 (2.80.1-0ubuntu2) ...
Setting up libblas3:amd64 (3.12.0-3build1) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up libpkgconf3:amd64 (1.8.1-2build1) ...
Setting up libasound2t64:amd64 (1.2.11-1build2) ...
Setting up libjaxen-java (1.1.6-4) ...
Setting up libapiguardian-java (1.1.2-1) ...
Setting up libfreetype6:amd64 (2.13.2+dfsg-1build3) ...
Setting up libx11-data (2:1.8.7-1build1) ...
Setting up libepoxy0:amd64 (1.5.10-1build1) ...
Setting up libnspr4:amd64 (2:4.35-1.1build1) ...
Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build7) ...
Setting up libjtidy-java (7+svn20110807-5) ...
Setting up libjansi-java (2.4.1-2) ...
Setting up libapache-pom-java (29-2) ...
Setting up libavahi-common-data:amd64 (0.8-13ubuntu6) ...
Setting up libxpp3-java (1.1.4c-3) ...
Setting up libatinject-jsr330-api-java (1.0+ds1-5) ...
Setting up libdbus-1-3:amd64 (1.14.10-4ubuntu4) ...
Setting up libwebsocket-api-java (1.1-2) ...
Setting up libfribidi0:amd64 (1.0.13-3build1) ...
Setting up libplexus-interpolation-java (1.26-1) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libxml-commons-resolver1.1-java (1.2-11) ...
Setting up libxz-java (1.9-1) ...
Setting up libitext1-java (1.4-7) ...
Setting up libio-html-perl (1.004-3) ...
Setting up libtcl8.6:amd64 (8.6.14+dfsg-1build1) ...
Setting up autopoint (0.21-14ubuntu2) ...
Setting up binfmt-support (2.2.2-7) ...
Running in chroot, ignoring request.
invoke-rc.d: policy-rc.d denied execution of start.
Created symlink '/etc/systemd/system/multi-user.target.wants/binfmt-support.service' → '/usr/lib/systemd/system/binfmt-support.service'.
Setting up libb-hooks-op-check-perl:amd64 (0.22-3build1) ...
Setting up keyboxd (2.4.4-2ubuntu17) ...
Created symlink '/etc/systemd/user/sockets.target.wants/keyboxd.socket' → '/usr/lib/systemd/user/keyboxd.socket'.
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libjbzip2-java (0.9.1-8) ...
Setting up libipc-run-perl (20231003.0-2) ...
Setting up libpcsclite1:amd64 (2.2.1-1) ...
Setting up ucf (3.0043+nmu1) ...
Setting up pkgconf-bin (1.8.1-2build1) ...
Setting up libsensors5:amd64 (1:3.6.0-9build1) ...
Setting up libmongodb-java (3.6.3-2) ...
Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ...
Setting up libactivation-java (1.2.0-2) ...
Setting up libhamcrest-java (2.2-2) ...
Setting up libglapi-mesa:amd64 (24.0.7-1ubuntu1) ...
Setting up libbsh-java (2.0b4-20) ...
Setting up libjsp-api-java (2.3.4-3) ...
Setting up libsasl2-2:amd64 (2.1.28+dfsg1-5ubuntu3) ...
Setting up libssh-4:amd64 (0.10.6-2build2) ...
Setting up libgfortran5:amd64 (14-20240429-1ubuntu1) ...
Setting up libvulkan1:amd64 (1.3.280.0-1) ...
Setting up autoconf (2.71-3) ...
Setting up libwebp7:amd64 (1.4.0-0.1) ...
Setting up libcolt-free-java (1.2.0+dfsg-8) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libicu74:amd64 (74.2-1ubuntu3) ...
Setting up libgif7:amd64 (5.2.2-1ubuntu1) ...
Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1ubuntu2) ...
Setting up dwz (0.15-1build6) ...
Setting up libfreemarker-java (2.3.32-2) ...
Setting up libxshmfence1:amd64 (1.3-1build5) ...
Setting up libjsoup-java (1.15.3-1) ...
Setting up at-spi2-common (2.52.0-1build1) ...
Setting up libcommons-math-java (2.2-8) ...
Setting up dbus-session-bus-common (1.14.10-4ubuntu4) ...
Setting up libuchardet0:amd64 (0.0.8-1build1) ...
Setting up libxml-commons-external-java (1.4.01-6) ...
Setting up libxbean-reflect-java (4.5-8) ...
Setting up libservlet-api-java (4.0.1-2) ...
Setting up librole-tiny-perl (2.002004-1) ...
Setting up libopentest4j-java (1.2.0-4) ...
Setting up debugedit (1:5.0-5build2) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libharfbuzz0b:amd64 (8.3.0-2build2) ...
Setting up ncbi-vdb-data (3.0.2+dfsg-2build2) ...
Setting up libthai-data (0.1.29-2build1) ...
Setting up netbase (6.4) ...
Setting up libcommons-math3-java (3.6.1-3) ...
Setting up sgml-base (1.31) ...
Setting up libsub-quote-perl (2.006008-1ubuntu1) ...
Setting up libclass-xsaccessor-perl (1.19-4build4) ...
Setting up libwagon-http-shaded-java (3.5.3-1) ...
Setting up libwayland-egl1:amd64 (1.22.0-2.1build1) ...
Setting up libhttpcore-java (4.4.16-1) ...
Setting up libjoptsimple-java (5.0.4-4) ...
Setting up ca-certificates-java (20240118) ...
No JRE found. Skipping Java certificates setup.
Setting up libprotoc32t64:amd64 (3.21.12-8.2build1) ...
Setting up libxerces2-java (2.12.2-1) ...
Setting up libfile-dirlist-perl (0.05-3) ...
Setting up dbus-system-bus-common (1.14.10-4ubuntu4) ...
Setting up libjaxp1.3-java (1.3.05-6) ...
Setting up libfile-homedir-perl (1.006-2) ...
Setting up libpj-java (0.0~20150107+dfsg-5) ...
Setting up libbsd0:amd64 (0.12.2-1) ...
Setting up libdrm-common (2.4.120-2build1) ...
Setting up libcdi-api-java (1.2-3) ...
Setting up libsnappy-jni (1.1.10.5-2) ...
Setting up libxml2:amd64 (2.9.14+dfsg-1.3ubuntu3) ...
Setting up xdg-utils (1.1.3-4.1ubuntu3) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up libldap2:amd64 (2.6.7+dfsg-1~exp1ubuntu8) ...
Setting up liburi-perl (5.28-1) ...
Setting up dbus-bin (1.14.10-4ubuntu4) ...
Setting up libfile-touch-perl (0.12-2) ...
Setting up dctrl-tools (2.24-3build3) ...
Setting up gnupg-utils (2.4.4-2ubuntu17) ...
Setting up libxkbcommon0:amd64 (1.6.0-1build1) ...
Setting up libwayland-client0:amd64 (1.22.0-2.1build1) ...
Setting up libnet-ssleay-perl:amd64 (1.94-1build4) ...
Setting up libjpeg8:amd64 (8c-2ubuntu11) ...
Setting up automake (1:1.16.5-1.3ubuntu1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libdom4j-java (2.1.4-1) ...
Setting up libjaxb-api-java (2.3.1-1) ...
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libwagon-provider-api-java (3.5.3-1) ...
Setting up libpaper1:amd64 (1.1.29build1) ...

Creating config file /etc/papersize with new version
Setting up libice6:amd64 (2:1.0.10-1build3) ...
Setting up libhttp-date-perl (6.06-1) ...
Setting up libxstream-java (1.4.20-1) ...
Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu6) ...
Setting up liblapack3:amd64 (3.12.0-3build1) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up libxcb1:amd64 (1.15-1ubuntu2) ...
Setting up gettext (0.21-14ubuntu2) ...
Setting up libmbedx509-1t64:amd64 (2.28.8-1) ...
Setting up libjetty9-java (9.4.54-1) ...
Setting up libxcb-xfixes0:amd64 (1.15-1ubuntu2) ...
Setting up java-wrappers (0.4) ...
Setting up libatk1.0-0t64:amd64 (2.52.0-1build1) ...
Setting up libfile-listing-perl (6.16-1) ...
Setting up libpython3.12-stdlib:amd64 (3.12.3-1) ...
Setting up libplexus-languages-java (1.1.1-2) ...
Setting up protobuf-compiler (3.21.12-8.2build1) ...
Setting up libjboss-vfs-java (3.2.15.Final-3) ...
Setting up jarwrapper (0.79) ...
Setting up libcurl4t64:amd64 (8.5.0-2ubuntu10.1) ...
Setting up libtool (2.4.7-7build1) ...
Setting up libxcb-render0:amd64 (1.15-1ubuntu2) ...
Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
Setting up libxcb-glx0:amd64 (1.15-1ubuntu2) ...
Setting up python3.12 (3.12.3-1) ...
Setting up libmaven-parent-java (35-1) ...
Setting up libedit2:amd64 (3.1-20230828-1build1) ...
Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:amd64 (0.8-13ubuntu6) ...
Setting up libcommons-logging-java (1.3.0-1ubuntu1) ...
Setting up libnet-http-perl (6.23-1) ...
Setting up libsisu-inject-java (0.3.4-2) ...
Setting up libnss3:amd64 (2:3.99-1) ...
Setting up libxcb-shm0:amd64 (1.15-1ubuntu2) ...
Setting up dbus-daemon (1.14.10-4ubuntu4) ...
Setting up libpaper-utils (1.1.29build1) ...
Setting up libdevel-callchecker-perl:amd64 (0.009-1) ...
Setting up libcommons-lang-java (2.6-10) ...
Setting up libcolord2:amd64 (1.4.7-1build2) ...
Setting up libplexus-cipher-java (2.0-1) ...
Setting up pkgconf:amd64 (1.8.1-2build1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libprotobuf-dev:amd64 (3.21.12-8.2build1) ...
Setting up libxcb-present0:amd64 (1.15-1ubuntu2) ...
Setting up libdconf1:amd64 (0.40.0-4build2) ...
Setting up dh-autoreconf (20) ...
Setting up libcommons-jexl2-java (2.1.1-6) ...
Setting up dirmngr (2.4.4-2ubuntu17) ...
Created symlink '/etc/systemd/user/sockets.target.wants/dirmngr.socket' → '/usr/lib/systemd/user/dirmngr.socket'.
Setting up libthai0:amd64 (0.1.29-2build1) ...
Setting up libsisu-plexus-java (0.3.4-3) ...
Setting up libllvm17t64:amd64 (1:17.0.6-12) ...
Setting up libxcb-sync1:amd64 (1.15-1ubuntu2) ...
Setting up libxalan2-java (2.7.2-4) ...
Setting up testng (6.9.12-4) ...
Setting up dbus (1.14.10-4ubuntu4) ...
Setting up shared-mime-info (2.4-4) ...
Setting up libcommons-collections4-java (4.4-2) ...
Setting up libcommons-lang3-java (3.14.0-1) ...
Setting up libxcb-dri2-0:amd64 (1.15-1ubuntu2) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libdrm2:amd64 (2.4.120-2build1) ...
Setting up libmaven-common-artifact-filters-java (3.3.2-1) ...
Setting up libmbedtls14t64:amd64 (2.28.8-1) ...
Setting up groff-base (1.23.0-4) ...
Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu2) ...
Setting up libwayland-cursor0:amd64 (1.22.0-2.1build1) ...
Setting up libxcb-randr0:amd64 (1.15-1ubuntu2) ...
Setting up libhtml-parser-perl:amd64 (3.82-1) ...
Setting up gnupg (2.4.4-2ubuntu17) ...
Setting up libpam-systemd:amd64 (256~rc1-1~exp2ubuntu1) ...
Setting up libcommons-beanutils-java (1.9.4-2) ...
Setting up libplexus-sec-dispatcher-java (2.0-3) ...
Setting up libx11-6:amd64 (2:1.8.7-1build1) ...
Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3ubuntu3) ...
Setting up libsnappy-java (1.1.10.5-2) ...
Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ...
Setting up libcommons-configuration-java (1.10-6) ...
Setting up libwagon-file-java (3.5.3-1) ...
Setting up libxml2-utils (2.9.14+dfsg-1.3ubuntu3) ...
Setting up libcommons-codec-java (1.16.0-1) ...
Setting up libxcomposite1:amd64 (1:0.4.5-1build3) ...
Setting up libsm6:amd64 (2:1.2.3-1build3) ...
Setting up libreflections-java (0.10.2+dfsg-2) ...
Setting up libavahi-client3:amd64 (0.8-13ubuntu6) ...
Setting up libio-socket-ssl-perl (2.085-1) ...
Setting up libpython3-stdlib:amd64 (3.12.3-0ubuntu1) ...
Setting up libhttp-message-perl (6.45-1ubuntu1) ...
Setting up libdrm-amdgpu1:amd64 (2.4.120-2build1) ...
Setting up libxcb-dri3-0:amd64 (1.15-1ubuntu2) ...
Setting up gtk-update-icon-cache (3.24.41-4ubuntu1) ...
Setting up libx11-xcb1:amd64 (2:1.8.7-1build1) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up velocity (1.7-7) ...
Setting up fontconfig (2.15.0-1.1ubuntu2) ...
Regenerating fonts cache... done.
Setting up libdrm-nouveau2:amd64 (2.4.120-2build1) ...
Setting up libxdamage1:amd64 (1:1.1.6-1build1) ...
Setting up openjdk-21-jre-headless:amd64 (21.0.3+9-1ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ...
Setting up libcommons-compress-java (1.25.0-1) ...
Setting up libhttp-cookies-perl (6.11-1) ...
Setting up libcommons-io-java (2.16.1-1) ...
Setting up libdrm-radeon1:amd64 (2.4.120-2build1) ...
Setting up libcommons-digester-java (1.8.1-6) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libdistlib-java (1.0-4) ...
Setting up libparams-classify-perl:amd64 (0.015-2build5) ...
Setting up libpango-1.0-0:amd64 (1.52.2+ds-1) ...
Setting up libdrm-intel1:amd64 (2.4.120-2build1) ...
Setting up libgl1-mesa-dri:amd64 (24.0.7-1ubuntu1) ...
Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2build2) ...
Setting up libxext6:amd64 (2:1.3.4-1build2) ...
Setting up libxmlgraphics-commons-java (2.8-2) ...
Setting up python3 (3.12.3-0ubuntu1) ...
Setting up man-db (2.12.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'.
Setting up libcairo2:amd64 (1.18.0-3build1) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1build4) ...
Setting up libmaven-filtering-java (3.3.0-1) ...
Setting up dbus-user-session (1.14.10-4ubuntu4) ...
Setting up libmaven-resolver-java (1.6.3-1) ...
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libxfixes3:amd64 (1:6.0.0-2build1) ...
Setting up libxinerama1:amd64 (2:1.1.4-3build1) ...
Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ...
Setting up libxrandr2:amd64 (2:1.5.4-1) ...
Setting up libhttpclient-java (4.5.14-1) ...
Setting up libmaven-dependency-tree-java (3.2.1-1) ...
Setting up liblightcouch-java (0.2.0-1) ...
Setting up libcairo-gobject2:amd64 (1.18.0-3build1) ...
Setting up libmaven-shared-utils-java (3.3.4-1) ...
Setting up libxss1:amd64 (1:1.2.3-1build3) ...
Setting up libpangoft2-1.0-0:amd64 (1.52.2+ds-1) ...
Setting up libmaven-resources-plugin-java (3.3.0-1) ...
Setting up libcups2t64:amd64 (2.4.7-1.2ubuntu7) ...
Setting up libpangocairo-1.0-0:amd64 (1.52.2+ds-1) ...
Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-6ubuntu5) ...
Setting up libngs-jni:amd64 (3.0.3+dfsg-6ubuntu5) ...
Setting up libxft2:amd64 (2.3.6-1build1) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libglx-mesa0:amd64 (24.0.7-1ubuntu1) ...
Setting up libxi6:amd64 (2:1.8.1-1build1) ...
Setting up libglx0:amd64 (1.7.0-1build1) ...
Setting up libcommons-validator-java (1:1.7-1) ...
Setting up libimport-into-perl (1.002005-2) ...
Setting up libxtst6:amd64 (2:1.2.3-1.1build1) ...
Setting up libbatik-java (1.17+dfsg-1) ...
Setting up libmoo-perl (2.005005-1) ...
Setting up liblog4j2-java (2.19.0-2) ...
Setting up libtk8.6:amd64 (8.6.14-1build1) ...
Setting up libxcursor1:amd64 (1:1.2.1-1build1) ...
Setting up libmaven-invoker-java (3.2.0-1) ...
Setting up debhelper (13.14.1ubuntu5) ...
Setting up dconf-service (0.40.0-4build2) ...
Setting up libgl1:amd64 (1.7.0-1build1) ...
Setting up libatspi2.0-0t64:amd64 (2.52.0-1build1) ...
Setting up r-base-core (4.4.0-2) ...

Creating config file /etc/R/Renviron with new version
Setting up libmaven-clean-plugin-java (3.2.0-2) ...
Setting up libplexus-archiver-java (4.6.1-1) ...
Setting up libngs-java:amd64 (3.0.3+dfsg-6ubuntu5) ...
Setting up libhtsjdk-java (4.1.0+dfsg-1) ...
Setting up libbarclay-java (5.0.0+dfsg-1) ...
Setting up libatk-bridge2.0-0t64:amd64 (2.52.0-1build1) ...
Setting up libfop-java (1:2.8-3) ...
Setting up dconf-gsettings-backend:amd64 (0.40.0-4build2) ...
Setting up libgkl-java (0.8.11+dfsg-2build1) ...
Setting up libmaven-archiver-java (3.6.0-1) ...
Setting up libpicard-java (3.1.1+dfsg-1) ...
Setting up libgtk-3-common (3.24.41-4ubuntu1) ...
Setting up liberror-prone-java (2.18.0-1) ...
Setting up libwww-perl (6.77-1) ...
Setting up devscripts (2.23.7ubuntu1) ...
Setting up libguava-java (32.0.1-1) ...
Setting up adwaita-icon-theme (46.0-1) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up libgtk-3-0t64:amd64 (3.24.41-4ubuntu1) ...
Setting up javahelper (0.79) ...
Setting up libprotobuf-java (3.21.12-8.2build1) ...
Setting up libplexus-container-default-java (2.1.1-1) ...
Setting up liblwp-protocol-https-perl (6.14-1) ...
Setting up libguice-java (4.2.3-2) ...
Setting up humanity-icon-theme (0.6.16) ...
Setting up libplexus-i18n-java (1.0-beta-10-6) ...
Setting up libplexus-container-default1.5-java (2.1.1-1) ...
Setting up libplexus-interactivity-api-java (1.1-2) ...
Setting up libplexus-velocity-java (1.2-3.1) ...
Setting up libmaven3-core-java (3.8.7-2) ...
Setting up libmaven-shared-incremental-java (1.1-4) ...
Setting up libmaven-shared-io-java (3.0.0-4) ...
Setting up ubuntu-mono (24.04-0ubuntu1) ...
Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ...
Setting up libmaven-dependency-analyzer-java (1.13.0-1) ...
Setting up libplexus-compiler-java (2.12.1-2) ...
Setting up libmaven-compiler-plugin-java (3.10.1-2) ...
Setting up libmaven-artifact-transfer-java (0.13.1-2) ...
Setting up libmaven-file-management-java (3.0.0-1) ...
Setting up libmaven-source-plugin-java (3.2.1-2) ...
Setting up libbyte-buddy-java (1.14.13-1) ...
Setting up libbuild-helper-maven-plugin-java (3.3.0-1) ...
Setting up libeasymock-java (5.2.0-1) ...
Setting up libmaven-jar-plugin-java (3.3.0-2) ...
Setting up libmaven-assembly-plugin-java (3.4.2-1) ...
Setting up libcommons-text-java (1.11.0-1) ...
Setting up libdoxia-core-java (1.12.0-1) ...
Setting up libdoxia-java (1.12.0-1) ...
Setting up libmaven-reporting-api-java (3.1.1-1) ...
Setting up libmaven-reporting-exec-java (1.6.0-1) ...
Processing triggers for libc-bin (2.39-0ubuntu8.1) ...
Processing triggers for systemd (256~rc1-1~exp2ubuntu1) ...
Processing triggers for ca-certificates-java (20240118) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem
Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:BJCA_Global_Root_CA1.pem
Adding debian:BJCA_Global_Root_CA2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:CommScope_Public_Trust_ECC_Root-01.pem
Adding debian:CommScope_Public_Trust_ECC_Root-02.pem
Adding debian:CommScope_Public_Trust_RSA_Root-01.pem
Adding debian:CommScope_Public_Trust_RSA_Root-02.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:ISRG_Root_X2.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem
Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem
Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_RootCA3.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Telia_Root_CA_v2.pem
Adding debian:TrustAsia_Global_Root_CA_G3.pem
Adding debian:TrustAsia_Global_Root_CA_G4.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:TunTrust_Root_CA.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up maven (3.8.7-2) ...
update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode
Setting up openjdk-21-jre:amd64 (21.0.3+9-1ubuntu1) ...
Setting up ant (1.10.14-1) ...
Setting up junit4 (4.13.2-4) ...
Setting up openjdk-21-jdk-headless:amd64 (21.0.3+9-1ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up default-jre-headless (2:1.21-75+exp1) ...
Setting up ant-contrib (1.0~b3+svn177-12) ...
Setting up maven-repo-helper (1.11) ...
Setting up default-jre (2:1.21-75+exp1) ...
Setting up libmaven-antrun-plugin-java (3.1.0-1) ...
Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ...
Setting up openjdk-21-jdk:amd64 (21.0.3+9-1ubuntu1) ...
update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up default-jdk-headless (2:1.21-75+exp1) ...
Setting up libjsap-java (2.1-5) ...
Setting up r-cran-rjava (1.0-11-1) ...
Setting up libdsiutils-java (2.7.3+dfsg-1) ...
Setting up junit5 (5.10.1-1) ...
Setting up default-jdk (2:1.21-75+exp1) ...
Setting up libicb-utils-java (2.0.1+git20161002.afee1d9-5) ...
Processing triggers for sgml-base (1.31) ...
Setting up libvelocity-tools-java (2.0-9) ...
Setting up libdoxia-sitetools-java (1.11.1-1) ...
Setting up libmaven-site-plugin-java (3.12.1-2) ...
Setting up libmaven-javadoc-plugin-java (3.4.1-3) ...
Setting up libmaven-reporting-impl-java (3.2.0-2) ...
Setting up libmaven-dependency-plugin-java (3.5.0-1) ...
Setting up libmaven-plugin-tools-java (3.7.1-1) ...
Setting up libsurefire-java (2.22.3-2) ...
Setting up maven-debian-helper (2.6.4) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (amd64 included in all)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 5.4.0-182-generic #202-Ubuntu SMP Fri Apr 26 12:29:36 UTC 2024 amd64 (x86_64)
Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu10 g++-13_13.2.0-25ubuntu1 gcc-13_13.2.0-25ubuntu1 libc6-dev_2.39-0ubuntu8.1 libstdc++-13-dev_13.2.0-25ubuntu1 libstdc++6_14-20240429-1ubuntu1 linux-libc-dev_6.8.0-31.31
Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 adwaita-icon-theme_46.0-1 ant_1.10.14-1 ant-contrib_1.0~b3+svn177-12 apt_2.9.3 apt-utils_2.9.3 at-spi2-common_2.52.0-1build1 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13.1ubuntu1 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.13.0-1 binfmt-support_2.2.2-7 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-x86-64-linux-gnu_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 ca-certificates-java_20240118 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-25ubuntu1 cpp-13-x86-64-linux-gnu_13.2.0-25ubuntu1 cpp-x86-64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 dbus_1.14.10-4ubuntu4 dbus-bin_1.14.10-4ubuntu4 dbus-daemon_1.14.10-4ubuntu4 dbus-session-bus-common_1.14.10-4ubuntu4 dbus-system-bus-common_1.14.10-4ubuntu4 dbus-user-session_1.14.10-4ubuntu4 dconf-gsettings-backend_0.40.0-4build2 dconf-service_0.40.0-4build2 dctrl-tools_2.24-3build3 debconf_1.5.86ubuntu1 debconf-i18n_1.5.86ubuntu1 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 default-jdk_2:1.21-75+exp1 default-jdk-headless_2:1.21-75+exp1 default-jre_2:1.21-75+exp1 default-jre-headless_2:1.21-75+exp1 devscripts_2.23.7ubuntu1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 dirmngr_2.4.4-2ubuntu17 dpkg_1.22.6ubuntu10 dpkg-dev_1.22.6ubuntu10 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.34-1 fastjar_2:0.98-7 file_1:5.45-3build1 findutils_4.9.0-5build1 fontconfig_2.15.0-1.1ubuntu2 fontconfig-config_2.15.0-1.1ubuntu2 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-25ubuntu1 g++-13-x86-64-linux-gnu_13.2.0-25ubuntu1 g++-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-25ubuntu1 gcc-13-base_13.2.0-25ubuntu1 gcc-13-x86-64-linux-gnu_13.2.0-25ubuntu1 gcc-14-base_14-20240429-1ubuntu1 gcc-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu2 gettext-base_0.21-14ubuntu2 gnupg_2.4.4-2ubuntu17 gnupg-utils_2.4.4-2ubuntu17 gpg_2.4.4-2ubuntu17 gpg-agent_2.4.4-2ubuntu17 gpgconf_2.4.4-2ubuntu17 gpgsm_2.4.4-2ubuntu17 gpgv_2.4.4-2ubuntu17 grep_3.11-4build1 groff-base_1.23.0-4 gtk-update-icon-cache_3.24.41-4ubuntu1 gzip_1.12-1ubuntu3 hicolor-icon-theme_0.17-2 hostname_3.23+nmu2ubuntu2 humanity-icon-theme_0.6.16 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 jarwrapper_0.79 java-common_0.75+exp1 java-wrappers_0.4 javahelper_0.79 junit4_4.13.2-4 junit5_5.10.1-1 keyboxd_2.4.4-2ubuntu17 krb5-locales_1.20.1-6ubuntu2 libacl1_2.3.2-2 libactivation-java_1.2.0-2 libaopalliance-java_20070526-7 libapache-pom-java_29-2 libapiguardian-java_1.1.2-1 libapparmor1_4.0.1-0ubuntu1 libapt-pkg6.0t64_2.9.3 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4build1 libasan8_14-20240429-1ubuntu1 libasm-java_9.7-1 libasound2-data_1.2.11-1build2 libasound2t64_1.2.11-1build2 libassuan0_2.5.6-1build1 libatinject-jsr330-api-java_1.0+ds1-5 libatk-bridge2.0-0t64_2.52.0-1build1 libatk1.0-0t64_2.52.0-1build1 libatomic1_14-20240429-1ubuntu1 libatspi2.0-0t64_2.52.0-1build1 libattr1_1:2.5.2-1build1 libaudit-common_1:3.1.2-2.1build1 libaudit1_1:3.1.2-2.1build1 libavahi-client3_0.8-13ubuntu6 libavahi-common-data_0.8-13ubuntu6 libavahi-common3_0.8-13ubuntu6 libb-hooks-op-check-perl_0.22-3build1 libbarclay-java_5.0.0+dfsg-1 libbatik-java_1.17+dfsg-1 libbinutils_2.42-4ubuntu2 libblas3_3.12.0-3build1 libblkid1_2.39.3-9ubuntu6 libbrotli1_1.1.0-2build2 libbsd0_0.12.2-1 libbsh-java_2.0b4-20 libbuild-helper-maven-plugin-java_3.3.0-1 libbyte-buddy-java_1.14.13-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-0ubuntu8.1 libc-dev-bin_2.39-0ubuntu8.1 libc6_2.39-0ubuntu8.1 libc6-dev_2.39-0ubuntu8.1 libcairo-gobject2_1.18.0-3build1 libcairo2_1.18.0-3build1 libcap-ng0_0.8.5-1 libcap2_1:2.66-5ubuntu2 libcc1-0_14-20240429-1ubuntu1 libcdi-api-java_1.2-3 libclass-method-modifiers-perl_2.15-1 libclass-xsaccessor-perl_1.19-4build4 libclone-perl_0.46-1build3 libcolord2_1.4.7-1build2 libcolt-free-java_1.2.0+dfsg-8 libcom-err2_1.47.0-2.4~exp1ubuntu4 libcommons-beanutils-java_1.9.4-2 libcommons-cli-java_1.6.0-1 libcommons-codec-java_1.16.0-1 libcommons-collections3-java_3.2.2-3 libcommons-collections4-java_4.4-2 libcommons-compress-java_1.25.0-1 libcommons-configuration-java_1.10-6 libcommons-digester-java_1.8.1-6 libcommons-exec-java_1.3-2 libcommons-io-java_2.16.1-1 libcommons-jexl2-java_2.1.1-6 libcommons-lang-java_2.6-10 libcommons-lang3-java_3.14.0-1 libcommons-logging-java_1.3.0-1ubuntu1 libcommons-math-java_2.2-8 libcommons-math3-java_3.6.1-3 libcommons-parent-java_56-1 libcommons-text-java_1.11.0-1 libcommons-validator-java_1:1.7-1 libcrypt-dev_1:4.4.36-4build1 libcrypt1_1:4.4.36-4build1 libcryptsetup12_2:2.7.0-1ubuntu4 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libcups2t64_2.4.7-1.2ubuntu7 libcurl4t64_8.5.0-2ubuntu10.1 libdatrie1_0.2.13-3build1 libdb5.3t64_5.3.28+dfsg2-7 libdbus-1-3_1.14.10-4ubuntu4 libdconf1_0.40.0-4build2 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdeflate0_1.20-1 libdevel-callchecker-perl_0.009-1 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdistlib-java_1.0-4 libdom4j-java_2.1.4-1 libdoxia-core-java_1.12.0-1 libdoxia-java_1.12.0-1 libdoxia-sitetools-java_1.11.1-1 libdpkg-perl_1.22.6ubuntu10 libdrm-amdgpu1_2.4.120-2build1 libdrm-common_2.4.120-2build1 libdrm-intel1_2.4.120-2build1 libdrm-nouveau2_2.4.120-2build1 libdrm-radeon1_2.4.120-2build1 libdrm2_2.4.120-2build1 libdsiutils-java_2.7.3+dfsg-1 libdw1t64_0.191-1 libdynaloader-functions-perl_0.003-3 libeasymock-java_5.2.0-1 libedit2_3.1-20230828-1build1 libel-api-java_3.0.0-3 libelf1t64_0.191-1 libencode-locale-perl_1.05-3 libepoxy0_1.5.10-1build1 liberror-prone-java_2.18.0-1 libexec-maven-plugin-java_3.1.0-2 libexpat1_2.6.2-1 libext2fs2t64_1.47.0-2.4~exp1ubuntu4 libfakeroot_1.34-1 libfastutil-java_8.5.12+dfsg-2 libfdisk1_2.39.3-9ubuntu6 libffi8_3.4.6-1build1 libfile-dirlist-perl_0.05-3 libfile-homedir-perl_1.006-2 libfile-listing-perl_6.16-1 libfile-stripnondeterminism-perl_1.13.1-1 libfile-touch-perl_0.12-2 libfile-which-perl_1.27-2 libfontbox2-java_2.0.29-1 libfontconfig1_2.15.0-1.1ubuntu2 libfop-java_1:2.8-3 libfreemarker-java_2.3.32-2 libfreetype6_2.13.2+dfsg-1build3 libfribidi0_1.0.13-3build1 libgatk-native-bindings-java_1.0.0+dfsg-2 libgcc-13-dev_13.2.0-25ubuntu1 libgcc-s1_14-20240429-1ubuntu1 libgcrypt20_1.10.3-2build1 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libgdk-pixbuf-2.0-0_2.42.10+dfsg-3ubuntu3 libgdk-pixbuf2.0-common_2.42.10+dfsg-3ubuntu3 libgeronimo-annotation-1.3-spec-java_1.3-1 libgeronimo-interceptor-3.0-spec-java_1.0.1-4fakesync libgfortran5_14-20240429-1ubuntu1 libgif7_5.2.2-1ubuntu1 libgkl-java_0.8.11+dfsg-2build1 libgl1_1.7.0-1build1 libgl1-mesa-dri_24.0.7-1ubuntu1 libglapi-mesa_24.0.7-1ubuntu1 libglib2.0-0t64_2.80.1-0ubuntu2 libglvnd0_1.7.0-1build1 libglx-mesa0_24.0.7-1ubuntu1 libglx0_1.7.0-1build1 libgmp10_2:6.3.0+dfsg-2ubuntu6 libgnutls30t64_3.8.5-2ubuntu1 libgomp1_14-20240429-1ubuntu1 libgoogle-gson-java_2.10.1-1 libgpg-error-l10n_1.49-2 libgpg-error0_1.49-2 libgpm2_1.20.7-11 libgprofng0_2.42-4ubuntu2 libgraphite2-3_1.3.14-2build1 libgssapi-krb5-2_1.20.1-6ubuntu2 libgtk-3-0t64_3.24.41-4ubuntu1 libgtk-3-common_3.24.41-4ubuntu1 libguava-java_32.0.1-1 libguice-java_4.2.3-2 libhamcrest-java_2.2-2 libharfbuzz0b_8.3.0-2build2 libhogweed6t64_3.9.1-2.2build1 libhtml-parser-perl_3.82-1 libhtml-tagset-perl_3.24-1 libhtml-tree-perl_5.07-3 libhtsjdk-java_4.1.0+dfsg-1 libhttp-cookies-perl_6.11-1 libhttp-date-perl_6.06-1 libhttp-message-perl_6.45-1ubuntu1 libhttp-negotiate-perl_6.01-2 libhttpclient-java_4.5.14-1 libhttpcore-java_4.4.16-1 libhwasan0_14-20240429-1ubuntu1 libicb-utils-java_2.0.1+git20161002.afee1d9-5 libice6_2:1.0.10-1build3 libicu4j-java_73.2-1 libicu74_74.2-1ubuntu3 libidn2-0_2.3.7-2build1 libimport-into-perl_1.002005-2 libio-html-perl_1.004-3 libio-pty-perl_1:1.20-1build2 libio-socket-ssl-perl_2.085-1 libip4tc2_1.8.10-3ubuntu2 libipc-run-perl_20231003.0-2 libisl23_0.26-3build1 libitext1-java_1.4-7 libitm1_14-20240429-1ubuntu1 libjansi-java_2.4.1-2 libjansson4_2.14-2build2 libjavassist-java_1:3.27.0-1 libjaxb-api-java_2.3.1-1 libjaxen-java_1.1.6-4 libjaxp1.3-java_1.3.05-6 libjbig0_2.1-6.1ubuntu2 libjboss-logging-java_3.5.3-1 libjboss-vfs-java_3.2.15.Final-3 libjbzip2-java_0.9.1-8 libjcommander-java_1.71-4 libjetty9-java_9.4.54-1 libjoptsimple-java_5.0.4-4 libjpeg-turbo8_2.1.5-2ubuntu2 libjpeg8_8c-2ubuntu11 libjsap-java_2.1-5 libjson-c5_0.17-1build1 libjsoup-java_1.15.3-1 libjsp-api-java_2.3.4-3 libjsr305-java_0.1~+svn49-11 libjtidy-java_7+svn20110807-5 libk5crypto3_1.20.1-6ubuntu2 libkeyutils1_1.6.3-3build1 libkmod2_31+20240202-2ubuntu7 libkrb5-3_1.20.1-6ubuntu2 libkrb5support0_1.20.1-6ubuntu2 libksba8_1.6.6-1build1 liblapack3_3.12.0-3build1 liblcms2-2_2.14-2build1 libldap2_2.6.7+dfsg-1~exp1ubuntu8 liblerc4_4.0.0+ds-4ubuntu2 liblightcouch-java_0.2.0-1 libllvm17t64_1:17.0.6-12 liblocale-gettext-perl_1.07-7 liblockfile-bin_1.17-1build3 liblockfile1_1.17-1build3 liblog4j1.2-java_1.2.17-11 liblog4j2-java_2.19.0-2 liblogback-java_1:1.2.11-5 liblsan0_14-20240429-1ubuntu1 liblwp-mediatypes-perl_6.04-2 liblwp-protocol-https-perl_6.14-1 liblz4-1_1.9.4-2 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3build1 libmagic1t64_1:5.45-3build1 libmaven-antrun-plugin-java_3.1.0-1 libmaven-archiver-java_3.6.0-1 libmaven-artifact-transfer-java_0.13.1-2 libmaven-assembly-plugin-java_3.4.2-1 libmaven-clean-plugin-java_3.2.0-2 libmaven-common-artifact-filters-java_3.3.2-1 libmaven-compiler-plugin-java_3.10.1-2 libmaven-dependency-analyzer-java_1.13.0-1 libmaven-dependency-plugin-java_3.5.0-1 libmaven-dependency-tree-java_3.2.1-1 libmaven-file-management-java_3.0.0-1 libmaven-filtering-java_3.3.0-1 libmaven-invoker-java_3.2.0-1 libmaven-jar-plugin-java_3.3.0-2 libmaven-javadoc-plugin-java_3.4.1-3 libmaven-parent-java_35-1 libmaven-plugin-tools-java_3.7.1-1 libmaven-reporting-api-java_3.1.1-1 libmaven-reporting-exec-java_1.6.0-1 libmaven-reporting-impl-java_3.2.0-2 libmaven-resolver-java_1.6.3-1 libmaven-resources-plugin-java_3.3.0-1 libmaven-shared-incremental-java_1.1-4 libmaven-shared-io-java_3.0.0-4 libmaven-shared-utils-java_3.3.4-1 libmaven-site-plugin-java_3.12.1-2 libmaven-source-plugin-java_3.2.1-2 libmaven3-core-java_3.8.7-2 libmbedcrypto7t64_2.28.8-1 libmbedtls14t64_2.28.8-1 libmbedx509-1t64_2.28.8-1 libmd0_1.1.0-2build1 libmjson-java_1.4.0-3 libmodule-runtime-perl_0.016-2 libmongodb-java_3.6.3-2 libmoo-perl_2.005005-1 libmount1_2.39.3-9ubuntu6 libmpc3_1.3.1-1build1 libmpfr6_4.2.1-1build1 libncbi-ngs3_3.0.3+dfsg-6ubuntu5 libncbi-vdb3_3.0.2+dfsg-2build2 libncursesw6_6.4+20240113-1ubuntu2 libnet-http-perl_6.23-1 libnet-ssleay-perl_1.94-1build4 libnettle8t64_3.9.1-2.2build1 libnghttp2-14_1.61.0-1 libngs-java_3.0.3+dfsg-6ubuntu5 libngs-jni_3.0.3+dfsg-6ubuntu5 libnpth0t64_1.6-3.1build1 libnsl-dev_1.3.0-3build3 libnsl2_1.3.0-3build3 libnspr4_2:4.35-1.1build1 libnss-nis_3.1-0ubuntu7 libnss-nisplus_1.3-5build1 libnss3_2:3.99-1 libobjenesis-java_3.3-3 libopentest4j-java_1.2.0-4 libopentest4j-reporting-java_0.1.0-M1-2 liboro-java_2.0.8a-14 libp11-kit0_0.25.3-4ubuntu2 libpam-modules_1.5.3-7ubuntu1 libpam-modules-bin_1.5.3-7ubuntu1 libpam-runtime_1.5.3-7ubuntu1 libpam-systemd_256~rc1-1~exp2ubuntu1 libpam0g_1.5.3-7ubuntu1 libpango-1.0-0_1.52.2+ds-1 libpangocairo-1.0-0_1.52.2+ds-1 libpangoft2-1.0-0_1.52.2+ds-1 libpaper-utils_1.1.29build1 libpaper1_1.1.29build1 libparams-classify-perl_0.015-2build5 libpciaccess0_0.17-3build1 libpcre2-8-0_10.42-4ubuntu2 libpcsclite1_2.2.1-1 libperl5.36_5.36.0-9ubuntu1 libperl5.38t64_5.38.2-4 libpicard-java_3.1.1+dfsg-1 libpicocli-java_4.6.2-2 libpipeline1_1.5.7-2 libpixman-1-0_0.42.2-1build1 libpj-java_0.0~20150107+dfsg-5 libpkgconf3_1.8.1-2build1 libplexus-ant-factory-java_1.0~alpha2.1-4 libplexus-archiver-java_4.6.1-1 libplexus-bsh-factory-java_1.0~alpha7-5 libplexus-build-api-java_0.0.7-4 libplexus-cipher-java_2.0-1 libplexus-classworlds-java_2.7.0-1 libplexus-compiler-java_2.12.1-2 libplexus-component-annotations-java_2.1.1-1 libplexus-container-default-java_2.1.1-1 libplexus-container-default1.5-java_2.1.1-1 libplexus-i18n-java_1.0-beta-10-6 libplexus-interactivity-api-java_1.1-2 libplexus-interpolation-java_1.26-1 libplexus-io-java_3.3.1-2 libplexus-languages-java_1.1.1-2 libplexus-sec-dispatcher-java_2.0-3 libplexus-utils2-java_3.4.2-1 libplexus-velocity-java_1.2-3.1 libpng16-16t64_1.6.43-5build1 libproc2-0_2:4.0.4-4ubuntu3 libprotobuf-dev_3.21.12-8.2build1 libprotobuf-java_3.21.12-8.2build1 libprotobuf-lite32t64_3.21.12-8.2build1 libprotobuf32t64_3.21.12-8.2build1 libprotoc32t64_3.21.12-8.2build1 libpsl5t64_0.21.2-1.1build1 libpython3-stdlib_3.12.3-0ubuntu1 libpython3.12-minimal_3.12.3-1 libpython3.12-stdlib_3.12.3-1 libqdox-java_1.12.1-3 libqdox2-java_2.0.3-1 libquadmath0_14-20240429-1ubuntu1 libreadline8t64_8.2-4build1 libreflections-java_0.10.2+dfsg-2 librhino-java_1.7.14-2.1 librole-tiny-perl_2.002004-1 librtmp1_2.4+20151223.gitfa8646d.1-2build7 libsasl2-2_2.1.28+dfsg1-5ubuntu3 libsasl2-modules-db_2.1.28+dfsg1-5ubuntu3 libseccomp2_2.5.5-1ubuntu3 libselinux1_3.5-2ubuntu2 libsemanage-common_3.5-1build5 libsemanage2_3.5-1build5 libsensors-config_1:3.6.0-9build1 libsensors5_1:3.6.0-9build1 libsepol2_3.5-2build1 libservlet-api-java_4.0.1-2 libsframe1_2.42-4ubuntu2 libsharpyuv0_1.4.0-0.1 libsisu-inject-java_0.3.4-2 libsisu-plexus-java_0.3.4-3 libslf4j-java_1.7.32-1 libsm6_2:1.2.3-1build3 libsmartcols1_2.39.3-9ubuntu6 libsnappy-java_1.1.10.5-2 libsnappy-jni_1.1.10.5-2 libsnappy1v5_1.2.0-2 libsqlite3-0_3.45.3-1 libss2_1.47.0-2.4~exp1ubuntu4 libssh-4_0.10.6-2build2 libssl3t64_3.0.13-0ubuntu3 libstdc++-13-dev_13.2.0-25ubuntu1 libstdc++6_14-20240429-1ubuntu1 libsub-override-perl_0.10-1 libsub-quote-perl_2.006008-1ubuntu1 libsurefire-java_2.22.3-2 libsystemd-shared_256~rc1-1~exp2ubuntu1 libsystemd0_256~rc1-1~exp2ubuntu1 libtasn1-6_4.19.0-3build1 libtcl8.6_8.6.14+dfsg-1build1 libtext-charwidth-perl_0.04-11build3 libtext-iconv-perl_1.7-8build3 libtext-wrapi18n-perl_0.06-10 libthai-data_0.1.29-2build1 libthai0_0.1.29-2build1 libtiff6_4.5.1+git230720-4ubuntu2 libtimedate-perl_2.3300-2 libtinfo6_6.4+20240113-1ubuntu2 libtirpc-common_1.3.4+ds-1.3 libtirpc-dev_1.3.4+ds-1.3 libtirpc3t64_1.3.4+ds-1.3 libtk8.6_8.6.14-1build1 libtool_2.4.7-7build1 libtry-tiny-perl_0.31-2 libtsan2_14-20240429-1ubuntu1 libubsan1_14-20240429-1ubuntu1 libuchardet0_0.0.8-1build1 libudev1_256~rc1-1~exp2ubuntu1 libunistring2_1.0-2 libunistring5_1.2-1 libunivocity-parsers-java_2.9.1-1 liburi-perl_5.28-1 libuuid1_2.39.3-9ubuntu6 libvelocity-tools-java_2.0-9 libvulkan1_1.3.280.0-1 libwagon-file-java_3.5.3-1 libwagon-http-shaded-java_3.5.3-1 libwagon-provider-api-java_3.5.3-1 libwayland-client0_1.22.0-2.1build1 libwayland-cursor0_1.22.0-2.1build1 libwayland-egl1_1.22.0-2.1build1 libwebp7_1.4.0-0.1 libwebsocket-api-java_1.1-2 libwww-perl_6.77-1 libwww-robotrules-perl_6.02-1 libx11-6_2:1.8.7-1build1 libx11-data_2:1.8.7-1build1 libx11-xcb1_2:1.8.7-1build1 libxalan2-java_2.7.2-4 libxau6_1:1.0.9-1build6 libxbean-reflect-java_4.5-8 libxcb-dri2-0_1.15-1ubuntu2 libxcb-dri3-0_1.15-1ubuntu2 libxcb-glx0_1.15-1ubuntu2 libxcb-present0_1.15-1ubuntu2 libxcb-randr0_1.15-1ubuntu2 libxcb-render0_1.15-1ubuntu2 libxcb-shm0_1.15-1ubuntu2 libxcb-sync1_1.15-1ubuntu2 libxcb-xfixes0_1.15-1ubuntu2 libxcb1_1.15-1ubuntu2 libxcomposite1_1:0.4.5-1build3 libxcursor1_1:1.2.1-1build1 libxdamage1_1:1.1.6-1build1 libxdmcp6_1:1.1.3-0ubuntu6 libxerces2-java_2.12.2-1 libxext6_2:1.3.4-1build2 libxfixes3_1:6.0.0-2build1 libxft2_2.3.6-1build1 libxi6_2:1.8.1-1build1 libxinerama1_2:1.1.4-3build1 libxkbcommon0_1.6.0-1build1 libxml-commons-external-java_1.4.01-6 libxml-commons-resolver1.1-java_1.2-11 libxml2_2.9.14+dfsg-1.3ubuntu3 libxml2-utils_2.9.14+dfsg-1.3ubuntu3 libxmlgraphics-commons-java_2.8-2 libxpp3-java_1.1.4c-3 libxrandr2_2:1.5.4-1 libxrender1_1:0.9.10-1.1build1 libxshmfence1_1.3-1build5 libxss1_1:1.2.3-1build3 libxstream-java_1.4.20-1 libxt6t64_1:1.2.1-1.2build1 libxtst6_2:1.2.3-1.1build1 libxxf86vm1_1:1.1.4-1build4 libxxhash0_0.8.2-2build1 libxz-java_1.9-1 libzstd1_1.5.5+dfsg2-2build1 linux-libc-dev_6.8.0-31.31 lockfile-progs_0.1.19+nmu1 login_1:4.13+dfsg1-4ubuntu3 logsave_1.47.0-2.4~exp1ubuntu4 lto-disabled-list_48 m4_1.4.19-4build1 make_4.3-4.1build2 man-db_2.12.1-1 maven_3.8.7-2 maven-debian-helper_2.6.4 maven-repo-helper_1.11 mawk_1.3.4.20240123-1build1 media-types_10.1.0 mount_2.39.3-9ubuntu6 ncbi-vdb-data_3.0.2+dfsg-2build2 ncurses-base_6.4+20240113-1ubuntu2 ncurses-bin_6.4+20240113-1ubuntu2 netbase_6.4 openjdk-21-jdk_21.0.3+9-1ubuntu1 openjdk-21-jdk-headless_21.0.3+9-1ubuntu1 openjdk-21-jre_21.0.3+9-1ubuntu1 openjdk-21-jre-headless_21.0.3+9-1ubuntu1 openssl_3.0.13-0ubuntu3 optipng_0.7.8+ds-1build2 passwd_1:4.13+dfsg1-4ubuntu3 patch_2.7.6-7build3 patchutils_0.4.2-1build3 perl_5.38.2-4 perl-base_5.38.2-4 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-4 perl-openssl-defaults_7build3 pinentry-curses_1.2.1-3ubuntu5 pkgbinarymangler_154 pkgconf_1.8.1-2build1 pkgconf-bin_1.8.1-2build1 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-4ubuntu3 protobuf-compiler_3.21.12-8.2build1 psmisc_23.7-1build1 python3_3.12.3-0ubuntu1 python3-minimal_3.12.3-0ubuntu1 python3.12_3.12.3-1 python3.12-minimal_3.12.3-1 r-base-core_4.4.0-2 r-cran-rjava_1.0-11-1 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu7 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2build1 sensible-utils_0.0.22 sgml-base_1.31 shared-mime-info_2.4-4 systemd_256~rc1-1~exp2ubuntu1 systemd-dev_256~rc1-1~exp2ubuntu1 systemd-sysv_256~rc1-1~exp2ubuntu1 sysvinit-utils_3.08-6ubuntu3 tar_1.35+dfsg-3build1 testng_6.9.12-4 tzdata_2024a-4ubuntu1 ubuntu-keyring_2023.11.28.1 ubuntu-mono_24.04-0ubuntu1 ucf_3.0043+nmu1 unzip_6.0-28ubuntu4 util-linux_2.39.3-9ubuntu6 uuid-runtime_2.39.3-9ubuntu6 velocity_1.7-7 wdiff_1.2.2-6build1 x11-common_1:7.7+23ubuntu3 xdg-utils_1.1.3-4.1ubuntu3 xkb-data_2.41-2ubuntu1 xz-utils_5.6.1+really5.4.5-1 zip_3.0-13build1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: libgoby-java
Binary: libgoby-io-java, goby-java
Architecture: all
Version: 3.3.1+dfsg2-11
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Pierre Gruet <pgt@debian.org>, Andreas Tille <tille@debian.org>
Homepage: https://campagnelab.org/software/goby/
Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/libgoby-java/
Vcs-Git: https://salsa.debian.org/med-team/libgoby-java.git
Testsuite: autopkgtest
Testsuite-Triggers: default-jdk
Build-Depends: debhelper-compat (= 13), maven-debian-helper, javahelper, default-jdk
Build-Depends-Indep: ant, ant-contrib, libjbzip2-java, libcommons-collections3-java, libcommons-configuration-java, libcommons-exec-java, libcommons-io-java, libcommons-lang-java, libcommons-logging-java, libcommons-math-java, libcommons-cli-java, libdistlib-java, liblog4j1.2-java, libexec-maven-plugin-java, libjaxb-api-java, libmaven-assembly-plugin-java, libmaven-antrun-plugin-java, libbuild-helper-maven-plugin-java, libmaven-dependency-plugin-java, libmaven-source-plugin-java, libmaven-javadoc-plugin-java, libprotobuf-java, libhtsjdk-java, libfastutil-java, protobuf-compiler, libjsap-java, libdsiutils-java, libicb-utils-java, libreflections-java, libpj-java, libprotobuf-dev, pkgconf, r-cran-rjava, libeasymock-java <!nocheck>, junit4 <!nocheck>, testng <!nocheck>, libpicard-java <!nocheck>
Package-List:
 goby-java deb science optional arch=all
 libgoby-io-java deb science optional arch=all
Checksums-Sha1:
 f9f9b6c1f4e76c9c403e1a9881d2c81f4d371d1c 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz
 b26ff390aa68ce3035d8153bb80f2153382882ec 29428 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz
Checksums-Sha256:
 b76b19808f893790e238c91e65680441ff020794cc7708ad6695cf13f0767148 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz
 db2427807fcc6967f7d3d85e656e4b219bd5af8e88faf8c21bdae07b6f74f468 29428 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz
Files:
 3a8dbf45ef2c54ec3073240850acbc75 41577532 libgoby-java_3.3.1+dfsg2.orig.tar.xz
 ee077d346354fb548086bf2a9f9f11e5 29428 libgoby-java_3.3.1+dfsg2-11.debian.tar.xz

-----BEGIN PGP SIGNATURE-----
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=36L5
-----END PGP SIGNATURE-----

gpgv: Signature made Tue May 14 16:31:58 2024 UTC
gpgv:                using RSA key 33CB284313E90BD27DCB4523600316A6DC277476
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./libgoby-java_3.3.1+dfsg2-11.dsc: no acceptable signature found
dpkg-source: info: extracting libgoby-java in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking libgoby-java_3.3.1+dfsg2.orig.tar.xz
dpkg-source: info: unpacking libgoby-java_3.3.1+dfsg2-11.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying protoc.patch
dpkg-source: info: applying adding_dependencies.patch
dpkg-source: info: applying using_jbzip2.patch
dpkg-source: info: applying adapting_to_old_fastutil.patch
dpkg-source: info: applying using_GeneratedMessageV3.patch
dpkg-source: info: applying using_commons-cli.patch
dpkg-source: info: applying using_correct_SamReader_api.patch
dpkg-source: info: applying inclusions_in_SplitTranscriptsMode.patch
dpkg-source: info: applying catch_IOException_LineIterator.patch
dpkg-source: info: applying computing_fisher_pvalue_hypergeom.patch
dpkg-source: info: applying exclude_not_runnable_tests.patch
dpkg-source: info: applying goby_script.patch
dpkg-source: info: applying path_of_goby_jar_for_Debian.patch
dpkg-source: info: applying jaxb_dependency.patch
dpkg-source: info: applying using_pcre2.patch
dpkg-source: info: applying omit_test_failing_randomly.patch
dpkg-source: info: applying adding_opens_arg_for_tests.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-28446411
SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28446411
SCHROOT_COMMAND=env
SCHROOT_GID=2501
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=build-PACKAGEBUILD-28446411
SCHROOT_UID=2001
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=unknown
USER=buildd
V=1

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon <buildd@lcy02-amd64-047.buildd> -b -rfakeroot
dpkg-buildpackage: info: source package libgoby-java
dpkg-buildpackage: info: source version 3.3.1+dfsg2-11
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --with javahelper
   dh_auto_clean
	bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done"
	mh_unpatchpoms -plibgoby-io-java
   jh_clean
   debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -rf goby-distribution/test-data goby-distribution/test-results
rm -rf test-results/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
 debian/rules binary
dh binary --with javahelper
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
	mh_patchpoms -plibgoby-io-java --debian-build --keep-pom-version --maven-repo=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian/maven-repo
   jh_linkjars
   dh_auto_build
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
[WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16
[WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
[WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Goby Framework                                                     [pom]
[INFO] Goby I/O                                                           [jar]
[INFO] Goby Full Distribution                                             [jar]
[INFO] 
[INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
[INFO] Building Goby Framework 3.3.1                                      [1/3]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
[INFO] Building Goby I/O 3.3.1                                            [2/3]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The artifact org.apache.maven.plugins:maven-resources-plugin:jar:2.6 has been relocated to org.apache.maven.plugins:maven-resources-plugin:jar:3.3.0
[WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3
[WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:2.4 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0
[INFO] 
[INFO] --- build-helper-maven-plugin:3.3.0:add-source (add-classes) @ goby-io ---
[INFO] Source directory: /<<PKGBUILDDIR>>/goby-io/target/generated-sources added.
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-java-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO]     [mkdir] Created dir: /<<PKGBUILDDIR>>/goby-io/target/generated-sources
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-io ---
[INFO] Copying 2 resources
[INFO] Copying 1 resource
[INFO] Copying 1 resource
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-io ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 260 source files to /<<PKGBUILDDIR>>/goby-io/target/classes
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (default) @ goby-io ---
[WARNING] Parameter tasks is deprecated, use target instead
[INFO] Executing tasks
[INFO]      [copy] Copying 1 file to /<<PKGBUILDDIR>>
[INFO]      [copy] Copying 1 file to /<<PKGBUILDDIR>>/goby-io/target/classes
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ goby-io ---
[INFO] skip non existing resourceDirectory /<<PKGBUILDDIR>>/goby-io/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-io ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-io ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ goby-io ---
[INFO] Building jar: /<<PKGBUILDDIR>>/goby-io/target/goby-io-3.3.1.jar
[INFO] 
[INFO] >>> maven-source-plugin:3.2.1:jar (attach-sources) > generate-sources @ goby-io >>>
[INFO] 
[INFO] --- build-helper-maven-plugin:3.3.0:add-source (add-classes) @ goby-io ---
[INFO] Source directory: /<<PKGBUILDDIR>>/goby-io/target/generated-sources added.
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-java-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] <<< maven-source-plugin:3.2.1:jar (attach-sources) < generate-sources @ goby-io <<<
[INFO] 
[INFO] 
[INFO] --- maven-source-plugin:3.2.1:jar (attach-sources) @ goby-io ---
[INFO] Building jar: /<<PKGBUILDDIR>>/goby-io/target/goby-io-3.3.1-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.4.1:jar (attach-javadocs) @ goby-io ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] Loading source files for package org.campagnelab.goby.predictions...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.ranges...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.dsv...
[WARNING] Loading source files for package org.campagnelab.goby.readers.sam...
[WARNING] Loading source files for package org.campagnelab.goby.readers...
[WARNING] Loading source files for package org.campagnelab.goby.readers.vcf...
[WARNING] Loading source files for package org.campagnelab.goby.reads...
[WARNING] Loading source files for package org.campagnelab.goby.modes...
[WARNING] Loading source files for package org.campagnelab.goby.modes.core...
[WARNING] Loading source files for package org.campagnelab.goby.modes.formats...
[WARNING] Loading source files for package org.campagnelab.goby.modes.dsv...
[WARNING] Loading source files for package org.campagnelab.goby.counts...
[WARNING] Loading source files for package org.campagnelab.goby.counts.compound...
[WARNING] Loading source files for package org.campagnelab.goby.alignments...
[WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk...
[WARNING] Loading source files for package org.campagnelab.goby.alignments.processors...
[WARNING] Loading source files for package org.campagnelab.goby.alignments.filters...
[WARNING] Loading source files for package org.campagnelab.goby.alignments.perms...
[WARNING] Loading source files for package org.campagnelab.goby...
[WARNING] Loading source files for package org.campagnelab.goby.R...
[WARNING] Loading source files for package org.campagnelab.goby.config...
[WARNING] Loading source files for package org.campagnelab.goby.parsers...
[WARNING] Loading source files for package org.campagnelab.goby.stats...
[WARNING] Loading source files for package org.campagnelab.goby.methylation...
[WARNING] Loading source files for package org.campagnelab.goby.cli...
[WARNING] Loading source files for package org.campagnelab.goby.exception...
[WARNING] Loading source files for package org.campagnelab.goby.baseinfo...
[WARNING] Loading source files for package org.campagnelab.goby.xml...
[WARNING] Loading source files for package org.campagnelab.goby.util...
[WARNING] Loading source files for package org.campagnelab.goby.util.commits...
[WARNING] Loading source files for package org.campagnelab.goby.util.pool...
[WARNING] Loading source files for package org.campagnelab.goby.util.motifs...
[WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions...
[WARNING] Loading source files for package org.campagnelab.goby.util.barcode...
[WARNING] Loading source files for package org.campagnelab.goby.compression...
[WARNING] Loading source files for package samples...
[WARNING] Loading source files for package org.campagnelab.dl.varanalysis.protobuf...
[WARNING] Constructing Javadoc information...
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java:22: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:21: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlAccessType;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:22: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlAccessorType;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol
[WARNING] @XmlAccessorType(XmlAccessType.FIELD)
[WARNING] ^
[WARNING] symbol: class XmlAccessorType
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:21: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlAccessType;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:22: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlAccessorType;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol
[WARNING] @XmlAccessorType(XmlAccessType.FIELD)
[WARNING] ^
[WARNING] symbol: class XmlAccessorType
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:22: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlElement;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:23: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlElementWrapper;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:24: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlRootElement;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:32: error: cannot find symbol
[WARNING] @XmlRootElement(name = "info-output")
[WARNING] ^
[WARNING] symbol: class XmlRootElement
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:30: error: package org.apache.commons.exec does not exist
[WARNING] import org.apache.commons.exec.CommandLine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:31: error: package org.apache.commons.exec does not exist
[WARNING] import org.apache.commons.exec.DefaultExecutor;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:32: error: package org.apache.commons.exec does not exist
[WARNING] import org.apache.commons.exec.PumpStreamHandler;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java:23: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:32: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.ParallelTeam;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:43: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBContext;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:44: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBException;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:45: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.Unmarshaller;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:76: error: cannot find symbol
[WARNING] private ParallelTeam team;
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class StatsMode
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java:23: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.PJProperties;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:34: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBContext;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:35: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBException;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:36: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.Marshaller;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:21: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlRootElement;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:31: error: cannot find symbol
[WARNING] @XmlRootElement
[WARNING] ^
[WARNING] symbol: class XmlRootElement
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:696: error: cannot find symbol
[WARNING] private void writeXml(PrintWriter output, String[] samples, MethylStats[] methylStats) throws JAXBException {
[WARNING] ^
[WARNING] symbol:   class JAXBException
[WARNING] location: class MethylStatsMode
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/TestRConnectionMode.java:25: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:39: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.IntegerForLoop;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:40: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.ParallelRegion;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:41: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.ParallelTeam;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:53: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBContext;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:54: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.JAXBException;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:55: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.Marshaller;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:106: error: cannot find symbol
[WARNING] private ParallelTeam team;
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class CompactAlignmentToAnnotationCountsMode
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:325: error: cannot find symbol
[WARNING] protected synchronized ParallelTeam getParallelTeam() {
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class CompactAlignmentToAnnotationCountsMode
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:441: error: cannot find symbol
[WARNING] private void writeInfoOutput() throws JAXBException, IOException {
[WARNING] ^
[WARNING] symbol:   class JAXBException
[WARNING] location: class CompactAlignmentToAnnotationCountsMode
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:283: error: cannot find symbol
[WARNING] class BasenameParallelRegion extends ParallelRegion {
[WARNING] ^
[WARNING] symbol:   class ParallelRegion
[WARNING] location: class CompactAlignmentToAnnotationCountsMode
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.java:42: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.java:45: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.java:40: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:24: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:56: error: cannot find symbol
[WARNING] private Rengine rengine;
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class GobyRengine
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:127: error: cannot find symbol
[WARNING] public Rengine getRengine() {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class GobyRengine
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:27: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.REXP;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:28: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.RVector;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:29: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:208: error: cannot find symbol
[WARNING] private static Result evaluateFisherExpression(final Rengine rengine,
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class FisherExact
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:21: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.RMainLoopCallbacks;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:22: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol
[WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks {
[WARNING] ^
[WARNING] symbol: class RMainLoopCallbacks
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:35: error: cannot find symbol
[WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:50: error: cannot find symbol
[WARNING] public void rBusy(final Rengine rengine, final int which) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:70: error: cannot find symbol
[WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:81: error: cannot find symbol
[WARNING] public void rShowMessage(final Rengine rengine, final String message) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol
[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol
[WARNING] public void rFlushConsole(final Rengine rengine) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol
[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol
[WARNING] public void rLoadHistory(final Rengine re, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:23: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.RMainLoopCallbacks;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:24: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:29: error: cannot find symbol
[WARNING] class RLoggerMainLoopCallback implements RMainLoopCallbacks {
[WARNING] ^
[WARNING] symbol: class RMainLoopCallbacks
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:42: error: cannot find symbol
[WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:57: error: cannot find symbol
[WARNING] public void rBusy(final Rengine rengine, final int which) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:77: error: cannot find symbol
[WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:88: error: cannot find symbol
[WARNING] public void rShowMessage(final Rengine rengine, final String message) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:99: error: cannot find symbol
[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:108: error: cannot find symbol
[WARNING] public void rFlushConsole(final Rengine rengine) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:118: error: cannot find symbol
[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:127: error: cannot find symbol
[WARNING] public void rLoadHistory(final Rengine re, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:26: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:68: error: cannot find symbol
[WARNING] Rengine rEngine;
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class FisherExactRCalculator
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java:21: error: package DistLib does not exist
[WARNING] import DistLib.hypergeometric;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AnnotationAveragingWriter.java:39: error: package org.rosuda.JRI does not exist
[WARNING] import org.rosuda.JRI.Rengine;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:21: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.ParallelTeam;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:33: error: cannot find symbol
[WARNING] private ParallelTeam team;
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class DoInParallel
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:47: error: cannot find symbol
[WARNING] protected synchronized ParallelTeam getParallelTeam() {
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class DoInParallel
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:23: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.IntegerForLoop;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:24: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.ParallelRegion;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:31: error: cannot find symbol
[WARNING] class BasenameParallelRegion extends ParallelRegion {
[WARNING] ^
[WARNING] symbol: class ParallelRegion
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol
[WARNING] @XmlAccessorType(XmlAccessType.FIELD)
[WARNING] ^
[WARNING] symbol: variable XmlAccessType
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol
[WARNING] @XmlAccessorType(XmlAccessType.FIELD)
[WARNING] ^
[WARNING] symbol: variable XmlAccessType
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:35: error: cannot find symbol
[WARNING] @XmlElement(name = "al")
[WARNING] ^
[WARNING] symbol:   class XmlElement
[WARNING] location: class InfoOutput
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:36: error: cannot find symbol
[WARNING] @XmlElementWrapper(name = "annotation-lengths")
[WARNING] ^
[WARNING] symbol:   class XmlElementWrapper
[WARNING] location: class InfoOutput
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:39: error: cannot find symbol
[WARNING] @XmlElement(name = "tc")
[WARNING] ^
[WARNING] symbol:   class XmlElement
[WARNING] location: class InfoOutput
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:40: error: cannot find symbol
[WARNING] @XmlElementWrapper(name = "total-counts")
[WARNING] ^
[WARNING] symbol:   class XmlElementWrapper
[WARNING] location: class InfoOutput
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 21.0.3+9-Ubuntu-1ubuntu1
[WARNING] Building tree for all the packages and classes...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/AbstractAlignmentEntryFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AbstractAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.TransferIds.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractCommandLineMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AbstractConcatAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractGobyMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/AbstractMethylationAdapter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/AbstractOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.WillKeepI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByPeakDistanceMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByRPKMDifferenceMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/AlignedCountNormalization.html...
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignedSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.CombinedLists.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/AlignmentHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentPositionComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/AlignmentQualityFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReader.html...
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactoryBase.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderImpl.html...
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollection.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollection.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollectionOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntry.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntryOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeader.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeaderOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndex.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndex.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndexOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHits.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHits.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHitsOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocation.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocationOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfo.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfoOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMapping.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMapping.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMappingOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfo.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfoOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntry.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntryOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariation.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariationOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentSliceHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.OutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToTextMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentToTextWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriterImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/AlleleFrequencyOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Annotation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/AnnotationAveragingWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountIterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AnnotationPenaltyMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/AnnotationRPKM.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/AnnotationsToCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/AnyTransitionCountsIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATGCCorrectionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/AtLeastAQuarterFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/AverageCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/AverageFisherRCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/BarcodeDecoderMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcherResult.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformation.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollection.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollection.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollectionOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfo.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfoOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequency.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequency.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequencyOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfo.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfoOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutput.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutputOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/BasenameUtils.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/BaseProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/BaseStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/BaseToStringHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/BenjaminiHochbergAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreAmbiguityAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreOnlyAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/BisulfiteConversionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/BonferroniAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingAlignmentWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingSamBamWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BuggyDeltaStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/BuildSequenceCacheMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.html...
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/By5BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/BZip2ChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CachingCountsArchiveReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ChiSquareTestAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/ChiSquareTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ChromosomeMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/ChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/ChunkCodecHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/CodecHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ColorSpaceConverter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnField.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnFields.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnMetaInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/Columns.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/CommitPropertiesStatAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/commits/CommitPropertyHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.html...
[WARNING] /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<'
[WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors).
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToReadSetMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToTranscriptCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactFileStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.OutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToSAMMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CompareAlignmentToGenomeMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataInput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataOutput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDirectoryEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.PROGRAM_MODE.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/CompressedRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCountInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeStartCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ConcatAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ConcatenateAlignmentMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ConcatenateCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/ConcatenatePermutations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/ConstantAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ConversionConfig.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ConvertSamBAMReadToGobyAlignment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CountArchiveToPeakAnnotationsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountBinningAdapterI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountBinningAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/CountCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerNoThresholdingEffect.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountIndexBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/CountRawSampleIdsCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsAggregatorI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsArchiveReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToBedGraphMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToUnionPeaksAnnotationMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToWiggleMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsArchiveWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsReaderI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriterHelperI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriterI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/CovariateInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CovariateStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/CoverageMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CumulativeArrayKeeperFast.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DataProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DefaultAlignmentProcessorFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/DefaultAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeltaStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeNovoDMRfinder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/DiffAlignmentMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionAnalysis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.ElementType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionResults.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DifferentiallyMethylatedRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/DifferentiallyMethylatedRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiploidFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/DiscoverSequenceVariantsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/DiscoverVariantPositionData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/DisplaySequenceVariationsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterBitSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/DoInParallel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/DualRandomAccessSequenceCache.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/DummyFormatConfigurator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyGenomeAlignmentTargetMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/DummyObservationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessorUnsorted.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/DummyTrueGenotypeHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/DumpTargetInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionClient.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/ElementIndexComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/EmpiricalPMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/EmpiricalPValueEstimator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/EntropicIndelArtifactFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/EntryFlagHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/EquivalentIndelRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EquivalentIndelRegionCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/EstimatedTestDistributions.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EvidenceCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ExportableAlignmentEntryData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ExportSplicingEvents.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ExtractSplicingEventsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/FalseDiscoveryRateMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/FastaParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderOrder1.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderPlus.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderOrder1.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderPlus.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/FastaToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FastSmallAndLog10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/FastXEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/FastXReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FDRAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.answer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.CompactFileType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/FileSlice.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/FilesToAttributesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/FisherExact.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/FisherExact.AlternativeHypothesis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/FisherExact.Result.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FisherExactRCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FisherExactTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FoldChangeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/FoldChangeForExonPairs.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FoldChangeMagnitudeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/FormatConfigurator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/FormatFieldCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF3.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.FormulaChoice.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FrequencyTable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/FromToFreq.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/GCProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/GenericToolsDriver.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/GeneTranscriptRelationships.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/GenomeAlignmentTargetMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/GenomeDebugHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/GenomicRange.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/GenotypeFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/GenotypePredictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/GenotypesOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/GobyAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/config/GobyConfiguration.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/GobyDriver.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/GobyException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/GobyQuickSeqvar.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/GobyRengine.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/GobyRuntimeException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/GobySamRecord.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/GobySamSegment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/GobyVersion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/GrepReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/GroupAssociations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/GroupComparison.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/GZipChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/GzipOutputStreamWithCustomLevel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/HeaderUtil.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/HeptamerInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HeptamerWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/HeptamerWeightsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HiCMerge.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/HTSJdkReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/HTSJDKReaderImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec1.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/IndelCountOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/InferSexFromAlignmentsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/InfoForTarget.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/InformativeColumns.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/InformativeDouble.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/InformativeNonZeroNonNaN.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Interval.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/InvalidChecksumException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/IOUtil.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/IsDone.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/IterateAlignmentsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/IterateSortedAlignmentsToPileup.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/KnownIndelSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/LastParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/LastToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/LeftOverFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/LinearBinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/LocalSortProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log2BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/Log2FoldChangeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/LogGCCorrectionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/LoggingOutputStream.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/LogIsConfigured.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/LongNamedCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/MakeBisulfiteFastaExample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MaxCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MedianCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/Merge.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/MergeCompactAlignmentsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.SplitIndel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/MessageChunksReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/MessageChunksWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/MethylationFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/MethylationRateDifferenceStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRegionsOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationSimilarityMatch.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationSite.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylationSiteIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylCountInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/MethylCountProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderFromRegionsOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderTestSupport.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylRateInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/MethylSimilarityScan.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/xml/MethylStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/MethylStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/MinCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/ModifyAlignmentsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/MotifMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/MoveToFrontCoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/MultiReads.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/NamedCounters.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/NormalizationMethod.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/NotCompressedChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/NoUpgradeAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/NullChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/NullResettableObjectPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.TypeOfPair.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/ObservedIndel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/OffsetCountsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/OneBinStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/OutputInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/OutputInfoFromWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/OverlapResult.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/ParseAlignmentEntriesCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/ParseAlignmentEntriesWithIndexCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/ParseReadsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PassThroughStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/Peak.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/PeakAggregator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReaderInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/PicardFastaIndexedSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/PlantIndels.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/PositionAdapter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/PositionBaseInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/PositionFacadeAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/PositionToBasesMap.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/PostBarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/PreBarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/Predictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/PrintWeights.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/ProtobuffCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/ProtoHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestMciProviderStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PVAlueProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/QFast.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/QualityEncoding.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/QualityScoreFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutationInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/QueueResettableObjectPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/RandomAccessAnnotations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceCache.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceTestSupport.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Range.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Ranges.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByEnd.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByStart.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadCodec2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadCodecImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/ReaderFastaParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReadGroupHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReadIndexStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/ReadNameToIndex.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReadOriginInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ReadQualityStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.MetaData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.MetaData.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.MetaDataOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadCollection.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadCollection.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadCollectionOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadEntry.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/Reads.ReadEntryOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ReadSetToTextMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsLoader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/ReadsToText.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsToTextWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ReadsToWeightsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/ReadsWriterImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ReadWithIndex.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/RealignmentProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ReferenceLocation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/ReformatCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/RegionAveragingWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/RegionWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/RegisterThis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/Release1_9_7_2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveBasesMatchingIndelsGenotypeFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveIndelArtifactsFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/RenameWeights.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/RepositionableInputStream.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/Resettable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/ResettableObjectPoolInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/RpkmLikeNormalizationMethod.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/RunParallelMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamComparison.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamComparisonInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SAMComparisonMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SamExtractReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/SamHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamPerPositionComparison.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/SampleCountCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/SampleCountInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/SamplePair.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/SamplePairEnumerator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SampleQualityScoresMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/SampleStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/SamRecordGenomicPositionComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SAMRecordIterable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/SamRecordParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/SamSequenceVariation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SAMToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SAMToCompactOldMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/ScanReferenceSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Segment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Base.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Base.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.BaseOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.ReferencePosition.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.ReferencePosition.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.ReferencePositionOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Sample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.Sample.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SampleOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformation.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationCollection.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationCollection.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationCollectionOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/SegmentInformationRecords.SegmentInformationOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/SequenceBaseInformationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/SequenceDigests.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/SequenceEncoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/SequenceVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.ReadIndexInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.Variation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStats2Mode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/SimulateBisulfiteReads.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SimulateReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SitesInFixedWindow.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToListIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToSortedReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SlidingCountArray.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SmallAndLog10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/SomaticPredictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/SomaticVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/Sort1Mode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SortedAnnotations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/SortIterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SortMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.Limits.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SplitCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SplitFastaMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SplitTranscriptsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat3StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat4StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5MciProviderStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorBaseQuality.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistancesToReadVariations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToEndOfRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToStartOfRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorInsertSizes.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorNumVariationsInRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorPairFlags.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryAlignedLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryPosition.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorReadMappingQuality.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorTargetAlignedLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/StatisticCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/StatisticComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/StatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/StrandBiasFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/StreamSignal.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/SubSequenceMotifMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/SuggestPositionSlicesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SummedCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/TabToColumnInfoMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/TallyBasesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/TallyReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/TestRConnectionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/TestSkipTo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/Timer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptBestScoreAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptsAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/TrimMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/TSVWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/TTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/UnboundedFifoPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/UnionDumpIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/UpgradeMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/UpgradeModeCore.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/UpgradeTo1_9_6.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/Variant.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/Variant.FromTo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/Variant.GobyIndelFromVCF.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/VariantMapCreator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/VariantMapHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.VCFPosition.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.SyntaxException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFSubsetMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFToGenotypeMapMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VCFToKnownIndelsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VcfToTabMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/VCFWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/VersionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/WarningCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/WeightCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/WeightParameters.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/WeightsInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/WiggleWindow.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/WithinGroupVariabilityMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/config/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/config/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/commits/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/commits/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/xml/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/xml/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/constant-values.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/serialized-form.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF3.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.WillKeepI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/ProtoHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/Predictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/SomaticPredictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.SplitIndel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/DummyTrueGenotypeHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/GenotypePredictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/RandomAccessAnnotations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/CoverageAnalysis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeStartCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/WeightCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountIterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCountInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SummedCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.FormulaChoice.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/GCProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HeptamerWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/BaseProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.ReadIndexInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.Variation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EvidenceCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/QFast.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HiCMerge.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EquivalentIndelRegionCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.answer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ExportSplicingEvents.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat4StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeNovoDMRfinder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/MethylationRateDifferenceStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DifferentiallyMethylatedRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SlidingCountArray.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log2BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/RegionAveragingWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ChiSquareTestAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CovariateStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat3StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/By5BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestMciProviderStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/LinearBinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.TypeOfPair.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SmallAndLog10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BuggyDeltaStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SitesInFixedWindow.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5MciProviderStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/AbstractMethylationAdapter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FastSmallAndLog10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FisherExactTestAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeltaStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CumulativeArrayKeeperFast.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/EstimatedDistribution.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PVAlueProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/OneBinStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PassThroughStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/class-use/EquivalentIndelRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/ReadWithIndex.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylRateInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Annotation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/AnnotationRPKM.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/GroupComparison.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/CovariateInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Interval.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylCountInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterBitSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/HeptamerInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByEnd.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByStart.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Segment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/SamplePairEnumerator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/WeightsInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Range.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Ranges.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/SampleTotalCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/AnnotationLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/InfoOutput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/DiscoverVariantPositionData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/SampleCountInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparison.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamSegment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SAMRecordIterable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamRecord.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/class-use/FastXReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/class-use/FastXEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/PicardFastaIndexedSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/CompressedRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadProtobuffCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceCache.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/MultiReads.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriterImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/QualityEncoding.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceDigests.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsToTextWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceEncoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodecImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceTestSupport.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/DualRandomAccessSequenceCache.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsLoader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaData.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.MetaDataOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntry.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadEntryOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollection.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollection.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/class-use/Reads.ReadCollectionOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactSamHelperMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SampleQualityScoresMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.TransferIds.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/RunParallelMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DummyFormatConfigurator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TabToColumnInfoMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SamExtractReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToBedGraphMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/InferSexFromAlignmentsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToTextMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByPeakDistanceMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/GobyDriver.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationPenaltyMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadQualityStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SuggestPositionSlicesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationsToCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ColorSpaceConverter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactOldMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/PercentMismatchesQualityFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/StatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByRPKMDifferenceMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/GenericToolsDriver.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToSAMMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/WeightParameters.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.VCFPosition.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BarcodeDecoderMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateAlignmentMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MethylationFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToGenotypeMapMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitTranscriptsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DiffAlignmentMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/IterateSortedAlignmentsToPileup.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.OutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToReadSetMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToWiggleMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SortMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToUnionPeaksAnnotationMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadSetToTextMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/WithinGroupVariabilityMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/UpgradeMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReadsToWeightsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FormatConfigurator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.OutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractCommandLineMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFSubsetMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FilesToAttributesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DiscoverSequenceVariantsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SAMComparisonMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CoverageMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountArchiveToPeakAnnotationsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactFileStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BuildSequenceCacheMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractGobyMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.Limits.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MergeCompactAlignmentsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompareAlignmentToGenomeMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/EmpiricalPMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VersionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SimulateReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/LastToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DisplaySequenceVariationsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/Sort1Mode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ExtractSplicingEventsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FastaToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TrimMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BisulfiteConversionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TallyBasesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VcfToTabMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MethylStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/HeptamerWeightsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TestRConnectionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitFastaMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStats2Mode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToAnnotationCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TallyReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToKnownIndelsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FalseDiscoveryRateMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/BaseStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToTranscriptCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ReformatCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRegionsOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/IndelCountOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/CompareGroupsVCFOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SomaticVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/BetweenGroupSequenceVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiploidFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CommonIndelArtifactFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/StrandBiasFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/GenotypeFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/QualityScoreFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/AtLeastAQuarterFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/IterateSortedAlignmentsListImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountIndexBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountAdaptiveBinningAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CachingCountsArchiveReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdapterI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/PositionAdapter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/OffsetCountsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/UnionAlgorithmSkeleton.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/UnionDumpIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/AnyTransitionCountsIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/PeakAggregator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReaderI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/Peak.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsAggregatorI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/WiggleWindow.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterHelperI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataOutput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDirectoryEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataInput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.PROGRAM_MODE.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReferenceLocation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingSamBamWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingAlignmentWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractConcatAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NoUpgradeAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/RepositionableInputStream.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionFacadeAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadOriginInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/LastParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentPositionComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionToBasesMap.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionBaseInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GobyAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/HTSJdkReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentSliceHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Merge.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/UpgradeTo1_9_6.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactoryBase.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadIndexStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SamRecordGenomicPositionComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SortIterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/DefaultAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/EntryFlagHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentToTextWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriterImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignedSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadGroupHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/FileSlice.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ScanReferenceSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatSortedAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ExportableAlignmentEntryData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GenomicRange.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndex.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndex.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndexOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AmbiguousLocation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AmbiguousLocation.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AmbiguousLocationOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentTooManyHits.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentTooManyHits.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentTooManyHitsOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.ReadOriginInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.ReadOriginInfo.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.ReadOriginInfoOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierInfo.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierInfoOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierMapping.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierMapping.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.IdentifierMappingOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentHeader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentHeader.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentHeaderOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.SequenceVariation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.SequenceVariation.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.SequenceVariationOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.RelatedAlignmentEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.RelatedAlignmentEntry.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.RelatedAlignmentEntryOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentEntry.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentEntryOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollection.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollection.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollectionOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/class-use/HTSJDKReaderImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DefaultAlignmentProcessorFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyGenomeAlignmentTargetMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/ObservedIndel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessorUnsorted.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/RealignmentProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/InfoForTarget.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/LocalSortProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/GenomeAlignmentTargetMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToListIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToSortedReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreAmbiguityAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/GeneTranscriptRelationships.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptsAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptBestScoreAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AbstractAlignmentEntryFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreOnlyAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AlignmentQualityFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ConcatenatePermutations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReaderInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ReadNameToIndex.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutationInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/class-use/GobyVersion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.Result.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.AlternativeHypothesis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/config/class-use/GobyConfiguration.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/class-use/FastaParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/class-use/ReaderFastaParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/BullardUpperQuartileNormalization.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/SamplePair.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/EmpiricalPValueEstimator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/Log2FoldChangeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DataProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AlignedCountNormalization.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FDRAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/ChiSquareTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionResults.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderFromRegionsOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FormatFieldCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactRCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.ElementType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DummyObservationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/VCFWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/BenjaminiHochbergAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionAnalysis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderTestSupport.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/CountRawSampleIdsCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/CountCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/EstimatedTestDistributions.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/TTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/RpkmLikeNormalizationMethod.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/BonferroniAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/SampleCountCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/TSVWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeNonZeroNonNaN.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AbstractOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/MinCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/SampleStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeMagnitudeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/ElementIndexComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/NormalizationMethod.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/RegionWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AnnotationAveragingWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeDouble.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AverageCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/AverageFisherRCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeColumns.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSite.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/PrintWeights.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/ReadsToText.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/DoInParallel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/SimulateBisulfiteReads.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/RenameWeights.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/FoldChangeForExonPairs.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/DumpTargetInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/MakeBisulfiteFastaExample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/TestSkipTo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/class-use/PlantIndels.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/class-use/GobyException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/class-use/GobyRuntimeException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorInsertSizes.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorPairFlags.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/BasenameUtils.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToEndOfRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorTargetAlignedLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorNumVariationsInRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToStartOfRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistancesToReadVariations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorBaseQuality.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorReadMappingQuality.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryAlignedLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/ConstantAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryPosition.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/CommitPropertiesStatAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/xml/class-use/MethylStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfoFromWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.CompactFileType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/StreamSignal.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/LongNamedCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Variant.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Variant.GobyIndelFromVCF.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Variant.FromTo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/IOUtil.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/FromToFreq.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/HeaderUtil.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapCreator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/NamedCounters.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/KnownIndelSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/WarningCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/SamSequenceVariation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/AlignmentHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/Timer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/UnboundedFifoPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/GrepReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/SamHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/CodecHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/LoggingOutputStream.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/LogIsConfigured.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/IsDone.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/GenomeDebugHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/class-use/BaseToStringHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/commits/class-use/CommitPropertyHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/QueueResettableObjectPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/ResettableObjectPoolInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/Resettable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/class-use/NullResettableObjectPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/class-use/MotifMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/class-use/SubSequenceMotifMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/RegisterThis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionRegistry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionClient.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcherResult.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/OverlapResult.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PostBarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PreBarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceBaseInfoCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/BZip2ChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec1.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodecHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/NotCompressedChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastBufferedMessageChunksReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/InvalidChecksumException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/GzipOutputStreamWithCustomLevel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ProtobuffCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceSegmentInfoCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/GZipChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/NullChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderOrder1.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderOrder1.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderPlus.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/MoveToFrontCoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderPlus.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/class-use/ParseReadsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePositionOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.BaseOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SampleOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollectionOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutputOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequency.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequency.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequencyOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfoOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfoOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.Builder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollectionOrBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/cli/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/compression/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/config/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/exception/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/methylation/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/core/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/parsers/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/predictions/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/R/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/reads/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/stats/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/commits/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/dynoptions/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/motifs/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/util/pool/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/org/campagnelab/goby/xml/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/samples/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/overview-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/deprecated-list.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/index.html...
[WARNING] Building index for all classes...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/allclasses-index.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/allpackages-index.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/index-all.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/search.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/overview-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-io/target/apidocs/help-doc.html...
[WARNING] 100 warnings
[INFO] Building jar: /<<PKGBUILDDIR>>/goby-io/target/goby-io-3.3.1-javadoc.jar
[INFO] 
[INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
[INFO] Building Goby Full Distribution 3.3.1                              [3/3]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-distribution ---
[INFO] Copying 3 resources
[INFO] Copying 72 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-distribution ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 525 source files to /<<PKGBUILDDIR>>/goby-distribution/target/classes
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractCommandLineMode.java: Some input files use unchecked or unsafe operations.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractCommandLineMode.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ goby-distribution ---
[INFO] skip non existing resourceDirectory /<<PKGBUILDDIR>>/goby-distribution/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-distribution ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 120 source files to /<<PKGBUILDDIR>>/goby-distribution/target/test-classes
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Some input files use or override a deprecated API.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Recompile with -Xlint:deprecation for details.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestRealignmentProcessor.java: Some input files use unchecked or unsafe operations.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestRealignmentProcessor.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-distribution ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ goby-distribution ---
[INFO] Building jar: /<<PKGBUILDDIR>>/goby-distribution/target/goby-distribution-3.3.1.jar
[INFO] 
[INFO] >>> maven-source-plugin:3.2.1:jar (attach-sources) > generate-sources @ goby-distribution >>>
[INFO] 
[INFO] <<< maven-source-plugin:3.2.1:jar (attach-sources) < generate-sources @ goby-distribution <<<
[INFO] 
[INFO] 
[INFO] --- maven-source-plugin:3.2.1:jar (attach-sources) @ goby-distribution ---
[INFO] Building jar: /<<PKGBUILDDIR>>/goby-distribution/target/goby-distribution-3.3.1-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.4.1:jar (attach-javadocs) @ goby-distribution ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] Loading source files for package org.campagnelab.goby.predictions...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.ranges...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.dsv...
[WARNING] Loading source files for package org.campagnelab.goby.readers.sam...
[WARNING] Loading source files for package org.campagnelab.goby.readers...
[WARNING] Loading source files for package org.campagnelab.goby.readers.vcf...
[WARNING] Loading source files for package org.campagnelab.goby.reads...
[WARNING] Loading source files for package org.campagnelab.goby.modes...
[WARNING] Loading source files for package org.campagnelab.goby.modes.core...
[WARNING] Loading source files for package org.campagnelab.goby.modes.formats...
[WARNING] Loading source files for package org.campagnelab.goby.modes.dsv...
[WARNING] Loading source files for package org.campagnelab.goby.counts...
[WARNING] Loading source files for package org.campagnelab.goby.counts.compound...
[WARNING] Loading source files for package org.campagnelab.goby.alignments...
[WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk...
[WARNING] Loading source files for package org.campagnelab.goby.alignments.processors...
[WARNING] Loading source files for package org.campagnelab.goby.alignments.filters...
[WARNING] Loading source files for package org.campagnelab.goby.alignments.perms...
[WARNING] Loading source files for package org.campagnelab.goby...
[WARNING] Loading source files for package org.campagnelab.goby.R...
[WARNING] Loading source files for package org.campagnelab.goby.config...
[WARNING] Loading source files for package org.campagnelab.goby.parsers...
[WARNING] Loading source files for package org.campagnelab.goby.stats...
[WARNING] Loading source files for package org.campagnelab.goby.methylation...
[WARNING] Loading source files for package org.campagnelab.goby.cli...
[WARNING] Loading source files for package org.campagnelab.goby.exception...
[WARNING] Loading source files for package org.campagnelab.goby.baseinfo...
[WARNING] Loading source files for package org.campagnelab.goby.xml...
[WARNING] Loading source files for package org.campagnelab.goby.util...
[WARNING] Loading source files for package org.campagnelab.goby.util.commits...
[WARNING] Loading source files for package org.campagnelab.goby.util.pool...
[WARNING] Loading source files for package org.campagnelab.goby.util.motifs...
[WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions...
[WARNING] Loading source files for package org.campagnelab.goby.util.barcode...
[WARNING] Loading source files for package org.campagnelab.goby.compression...
[WARNING] Loading source files for package samples...
[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 21.0.3+9-Ubuntu-1ubuntu1
[WARNING] Building tree for all the packages and classes...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/AbstractAlignmentEntryFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AbstractAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.TransferIds.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractCommandLineMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AbstractConcatAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractGobyMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/AbstractMethylationAdapter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AbstractOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.WillKeepI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByPeakDistanceMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByRPKMDifferenceMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AlignedCountNormalization.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignedSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.CombinedLists.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/AlignmentHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentPositionComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/AlignmentQualityFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReader.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactoryBase.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderImpl.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentSliceHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.OutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToTextMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentToTextWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriterImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/AlleleFrequencyOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Annotation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AnnotationAveragingWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountIterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AnnotationPenaltyMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/AnnotationRPKM.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AnnotationsToCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/AnyTransitionCountsIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATGCCorrectionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/AtLeastAQuarterFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AverageCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AverageFisherRCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BarcodeDecoderMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcherResult.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/BasenameUtils.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/BaseProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BaseStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/BaseToStringHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BenjaminiHochbergAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreAmbiguityAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreOnlyAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BisulfiteConversionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BonferroniAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingAlignmentWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingSamBamWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BuggyDeltaStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BuildSequenceCacheMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/By5BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/BZip2ChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CachingCountsArchiveReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ChiSquareTestAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/ChiSquareTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ChromosomeMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ChunkCodecHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/CodecHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ColorSpaceConverter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnField.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnFields.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnMetaInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/Columns.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/CommitPropertiesStatAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/CommitPropertyHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<'
[WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors).
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToReadSetMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToTranscriptCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactFileStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.OutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToSAMMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompareAlignmentToGenomeMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataInput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataOutput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDirectoryEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.PROGRAM_MODE.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/CompressedRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCountInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeStartCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateAlignmentMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ConcatenatePermutations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/ConstantAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConversionConfig.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConvertSamBAMReadToGobyAlignment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountArchiveToPeakAnnotationsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdapterI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/CountCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerNoThresholdingEffect.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountIndexBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/CountRawSampleIdsCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsAggregatorI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsArchiveReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToBedGraphMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToUnionPeaksAnnotationMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToWiggleMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsArchiveWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsReaderI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriterHelperI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountsWriterI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/CovariateInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CovariateStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CoverageMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CumulativeArrayKeeperFast.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DataProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DefaultAlignmentProcessorFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/DefaultAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeltaStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeNovoDMRfinder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DiffAlignmentMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionAnalysis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.ElementType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionResults.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DifferentiallyMethylatedRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/DifferentiallyMethylatedRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/DiploidFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DiscoverSequenceVariantsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/DiscoverVariantPositionData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DisplaySequenceVariationsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterBitSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/DoInParallel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/DualRandomAccessSequenceCache.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/DummyFormatConfigurator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DummyGenomeAlignmentTargetMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/DummyObservationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessorUnsorted.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/DummyTrueGenotypeHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/DumpTargetInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionClient.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/ElementIndexComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/EmpiricalPMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/EmpiricalPValueEstimator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/EntropicIndelArtifactFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/EntryFlagHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/EquivalentIndelRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EquivalentIndelRegionCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/EstimatedTestDistributions.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/EvidenceCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ExportableAlignmentEntryData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ExportSplicingEvents.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ExtractSplicingEventsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FalseDiscoveryRateMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/FastaParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoder.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticCoder.java:56: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder
[WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J).
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderOrder1.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticCoderPlus.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoder.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java:33: warning: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder
[WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J)
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderI.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS
[WARNING] * the call, exactly {@link #BITS} excess bits will be present in the
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:60: warning: @return tag cannot be used in method with void return type.
[WARNING] void flush(InputBitStream ibs) throws IOException;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS
[WARNING] * @return the current bit stream window in the lower {@link #BITS} bits.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderOrder1.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS
[WARNING] * the call, exactly {@link #BITS} excess bits will be present in the
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS
[WARNING] * @return the current bit stream window in the lower {@link #BITS} bits.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastArithmeticDecoderPlus.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: reference not found: #BITS
[WARNING] * the call, exactly {@link #BITS} excess bits will be present in the
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: reference not found: #BITS
[WARNING] * @return the current bit stream window in the lower {@link #BITS} bits.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FastaToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FastSmallAndLog10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/FastXEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/FastXReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FDRAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FenwickTree.answer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/FileExtensionHelper.CompactFileType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/FileSlice.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FilesToAttributesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/FisherExact.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/FisherExact.AlternativeHypothesis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/FisherExact.Result.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FisherExactRCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FisherExactTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FoldChangeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/FoldChangeForExonPairs.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FoldChangeMagnitudeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FormatConfigurator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FormatFieldCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF3.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.FormulaChoice.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FrequencyTable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/FromToFreq.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/GCProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/GenericToolsDriver.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/GeneTranscriptRelationships.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/GenomeAlignmentTargetMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/GenomeDebugHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/GenomicRange.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/GenotypeFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/GenotypePredictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/GenotypesOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/GobyAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/config/GobyConfiguration.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:72: warning: reference not found: org.campagnelab.goby.aligners.LastagAligner
[WARNING] * @see org.campagnelab.goby.aligners.LastagAligner
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:79: warning: reference not found: org.campagnelab.goby.aligners.LastAligner
[WARNING] * @see org.campagnelab.goby.aligners.LastAligner
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:87: warning: reference not found: org.campagnelab.goby.aligners.BWAAligner
[WARNING] * @see org.campagnelab.goby.aligners.BWAAligner
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:95: warning: reference not found: org.campagnelab.goby.aligners.GSnapAligner
[WARNING] * @see org.campagnelab.goby.aligners.GSnapAligner
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/GobyDriver.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/GobyException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobyQuickSeqvar.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/GobyRengine.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/GobyRuntimeException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobySamRecord.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobySamSegment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/GobyVersion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/GrepReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/GroupAssociations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/GroupComparison.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/GZipChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/GzipOutputStreamWithCustomLevel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/HeaderUtil.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/HeptamerInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HeptamerWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/HeptamerWeightsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HiCMerge.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
[WARNING] * Dequeues a document from the queue, returning an instance of {@link
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
[WARNING] * Dequeues a document from the queue, returning an instance of {@link
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:131: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
[WARNING] * @return the next {@link edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore}.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/HTSJdkReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/HTSJDKReaderImpl.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec1.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/IndelCountOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/InferSexFromAlignmentsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/InfoForTarget.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeColumns.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeDouble.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeNonZeroNonNaN.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Interval.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/InvalidChecksumException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/IOUtil.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/IsDone.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/IterateAlignmentsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/IterateSortedAlignmentsToPileup.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/KnownIndelSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/LastParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/LastToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/LeftOverFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/LinearBinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/LocalSortProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log2BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/Log2FoldChangeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/LogGCCorrectionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/LoggingOutputStream.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/LogIsConfigured.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/LongNamedCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/MakeBisulfiteFastaExample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MaxCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MedianCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/Merge.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MergeCompactAlignmentsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.SplitIndel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylationFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/MethylationRateDifferenceStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRegionsOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSimilarityMatch.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSite.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSiteIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylCountInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderFromRegionsOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderTestSupport.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylRateInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylSimilarityScan.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/xml/MethylStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MinCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/ModifyAlignmentsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/MotifMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MoveToFrontCoder.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning: invalid input: '<'
[WARNING] * @param symbol Symbol to encode with move to front (precondition: 0<= symbol <numberOfSymbols).
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning: invalid input: '<'
[WARNING] * @param symbol Symbol to encode with move to front (precondition: 0<= symbol <numberOfSymbols).
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:43: warning: invalid input: '<'
[WARNING] * @return encoded symbol (post-condition: 0<= encoded-symbol <numberOfSymbols).
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:43: warning: invalid input: '<'
[WARNING] * @return encoded symbol (post-condition: 0<= encoded-symbol <numberOfSymbols).
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/MultiReads.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/NamedCounters.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReader.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/NormalizationMethod.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/NotCompressedChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/NoUpgradeAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/NullChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/NullResettableObjectPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.TypeOfPair.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/ObservedIndel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/OffsetCountsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/OneBinStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/OutputInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/OutputInfoFromWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/OverlapResult.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/ParseAlignmentEntriesCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/ParseAlignmentEntriesWithIndexCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/ParseReadsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PassThroughStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/Peak.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/PeakAggregator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReaderInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/PicardFastaIndexedSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/PlantIndels.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/PositionAdapter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/PositionBaseInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/PositionFacadeAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/PositionToBasesMap.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/PostBarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/PreBarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/Predictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/PrintWeights.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ProtobuffCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/ProtoHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestMciProviderStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&rct'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&q'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&esrc'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&source'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&cd'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&cts'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&ved'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&url'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&ei'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&usg'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&sig2'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PVAlueProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/QFast.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/QualityEncoding.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/QualityEncoding.java:41: warning: invalid input: '&'
[WARNING] * !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/QualityEncoding.java:41: warning: invalid input: '<'
[WARNING] * !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/QualityScoreFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutationInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/QueueResettableObjectPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/RandomAccessAnnotations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceCache.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceTestSupport.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Range.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Ranges.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByEnd.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByStart.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodecImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/ReaderFastaParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadGroupHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadIndexStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ReadNameToIndex.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadOriginInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadQualityStatsMode.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<'
[WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<'
[WARNING] * Number of reads skipped because of sampleFraction value < 1.0d.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<'
[WARNING] * Number of reads skipped because of sampleFraction value < 1.0d.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<'
[WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadSetToTextMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsLoader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/ReadsToText.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsToTextWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadsToWeightsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriterImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ReadWithIndex.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/RealignmentProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReferenceLocation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReformatCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/RegionAveragingWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RegionWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/RegisterThis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/Release1_9_7_2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveBasesMatchingIndelsGenotypeFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveIndelArtifactsFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/RenameWeights.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/RepositionableInputStream.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/Resettable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/ResettableObjectPoolInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RpkmLikeNormalizationMethod.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/RunParallelMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparison.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparison.java:233: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setCountComparisonFailures(final boolean countComparisonFailures) {
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparison.java:275: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setAllowSourceNs(boolean allowSourceNs) {
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparisonInterface.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparisonInterface.java:130: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setAllowSourceNs(boolean allowSourceNs);
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMComparisonMode.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java:214: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setCheckMate(final boolean checkMate) {
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SamExtractReadsMode.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning: invalid input: '<'
[WARNING] * WARNING: If the file contains pairs, the source SAM/BAM file >>MUST<< be sorted by read name.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning: invalid input: '<'
[WARNING] * WARNING: If the file contains pairs, the source SAM/BAM file >>MUST<< be sorted by read name.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamPerPositionComparison.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SampleCountCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/SampleCountInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SamplePair.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/SamplePairEnumerator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SampleQualityScoresMode.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java:176: warning: invalid input: '<'
[WARNING] * Set to <= 0 to process the entire file.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SampleStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SamRecordGenomicPositionComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SAMRecordIterable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamRecordParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamSequenceVariation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactOldMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ScanReferenceSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Segment.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '&'
[WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '&'
[WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end;
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '<'
[WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end;
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceBaseInformationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceDigests.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceEncoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.ReadIndexInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.Variation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStats2Mode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/SimulateBisulfiteReads.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SimulateReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SitesInFixedWindow.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToListIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToSortedReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SlidingCountArray.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SmallAndLog10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/SomaticPredictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SomaticVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/Sort1Mode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SortedAnnotations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SortIterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SortMode.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/SortMode.java:142: warning: invalid input: '<'
[WARNING] * Set to < 0 for auto-detect number of cores.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.Limits.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitFastaMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitTranscriptsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat3StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat4StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5MciProviderStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorBaseQuality.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistancesToReadVariations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToEndOfRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToStartOfRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorInsertSizes.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorNumVariationsInRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorPairFlags.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryAlignedLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryPosition.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorReadMappingQuality.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorTargetAlignedLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/StatisticCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/StatisticComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/StatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/StrandBiasFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/StreamSignal.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/SubSequenceMotifMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SuggestPositionSlicesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SummedCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TabToColumnInfoMode.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyBasesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TestRConnectionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/TestSkipTo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/Timer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptBestScoreAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptsAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TrimMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TSVWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/UnboundedFifoPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionDumpIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/UpgradeMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/UpgradeModeCore.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/UpgradeTo1_9_6.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.FromTo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.GobyIndelFromVCF.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/VariantMapCreator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/VariantMapHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.VCFPosition.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/readers/vcf/VCFParser.java:179: warning: invalid input: '<'
[WARNING] * Set to <= 0 to scan the entire file. This must be set before calling readHeader() for the value to be used.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.SyntaxException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFSubsetMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFToGenotypeMapMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFToKnownIndelsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VcfToTabMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/VCFWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VersionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/WarningCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/WeightCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/WeightParameters.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/WeightsInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/WiggleWindow.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/WithinGroupVariabilityMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/config/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/config/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/xml/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/xml/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/package-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/package-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/constant-values.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/serialized-form.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/SomaticPredictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/Predictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.WillKeepI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/GenotypePredictor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/DummyTrueGenotypeHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/ProtoHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF3.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.SplitIndel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EquivalentIndelRegionCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/RandomAccessAnnotations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/CoverageAnalysis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeStartCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/WeightCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountIterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCountInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SummedCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.FormulaChoice.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/GCProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HeptamerWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/BaseProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.ReadIndexInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.Variation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EvidenceCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/QFast.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HiCMerge.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.answer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ExportSplicingEvents.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat4StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeNovoDMRfinder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/MethylationRateDifferenceStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DifferentiallyMethylatedRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SlidingCountArray.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log2BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/RegionAveragingWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ChiSquareTestAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CovariateStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat3StatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/By5BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestMciProviderStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/LinearBinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.TypeOfPair.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SmallAndLog10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BuggyDeltaStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SitesInFixedWindow.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5MciProviderStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/AbstractMethylationAdapter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FastSmallAndLog10BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FisherExactTestAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeltaStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BinningStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CumulativeArrayKeeperFast.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/EstimatedDistribution.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PVAlueProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/OneBinStrategy.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PassThroughStatisticAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/class-use/EquivalentIndelRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/ReadWithIndex.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylRateInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Annotation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/AnnotationRPKM.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/GroupComparison.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/CovariateInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Interval.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/MethylCountInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterBitSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/HeptamerInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByEnd.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Read.ReadSortByStart.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Segment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/SamplePairEnumerator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/WeightsInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Range.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Ranges.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/SampleTotalCount.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/AnnotationLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/InfoOutput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/DiscoverVariantPositionData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/class-use/SampleCountInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SAMRecordIterable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparison.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamSegment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamRecord.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriterImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadProtobuffCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/PicardFastaIndexedSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/DualRandomAccessSequenceCache.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsToTextWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceEncoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodecImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/QualityEncoding.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceCache.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsLoader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceTestSupport.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceDigests.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/CompressedRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/MultiReads.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactSamHelperMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SampleQualityScoresMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.TransferIds.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/RunParallelMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DummyFormatConfigurator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TabToColumnInfoMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SamExtractReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToBedGraphMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/InferSexFromAlignmentsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToTextMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByPeakDistanceMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GobyDriver.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationPenaltyMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadQualityStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SuggestPositionSlicesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationsToCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ColorSpaceConverter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactOldMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/PercentMismatchesQualityFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/StatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByRPKMDifferenceMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GenericToolsDriver.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToSAMMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/WeightParameters.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.VCFPosition.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BarcodeDecoderMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateAlignmentMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MethylationFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToGenotypeMapMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitTranscriptsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DiffAlignmentMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/IterateSortedAlignmentsToPileup.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.OutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToReadSetMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToWiggleMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SortMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToUnionPeaksAnnotationMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadSetToTextMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/WithinGroupVariabilityMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/UpgradeMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadsToWeightsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FormatConfigurator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.OutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractCommandLineMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFSubsetMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FilesToAttributesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DiscoverSequenceVariantsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMComparisonMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CoverageMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountArchiveToPeakAnnotationsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactFileStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BuildSequenceCacheMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractGobyMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.Limits.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MergeCompactAlignmentsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompareAlignmentToGenomeMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/EmpiricalPMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VersionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SimulateReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/LastToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DisplaySequenceVariationsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/Sort1Mode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ExtractSplicingEventsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FastaToCompactMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TrimMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BisulfiteConversionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyBasesMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VcfToTabMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MethylStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/HeptamerWeightsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TestRConnectionMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitFastaMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStats2Mode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToAnnotationCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToKnownIndelsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FalseDiscoveryRateMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BaseStatsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToTranscriptCountsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReformatCompactReadsMode.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRegionsOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/IndelCountOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/CompareGroupsVCFOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SomaticVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/BetweenGroupSequenceVariationOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiploidFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CommonIndelArtifactFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/StrandBiasFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/GenotypeFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/QualityScoreFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/AtLeastAQuarterFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/IterateSortedAlignmentsListImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/OffsetCountsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/AnyTransitionCountsIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/Peak.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountIndexBuilder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/WiggleWindow.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/UnionAlgorithmSkeleton.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/PeakAggregator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsAggregatorI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdapterI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/UnionDumpIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/PositionAdapter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriterHelperI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CachingCountsArchiveReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountBinningAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsArchiveWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountAdaptiveBinningAdaptor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountWriterHelper2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReaderI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataOutput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDirectoryEntry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundDataInput.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/class-use/CompoundFileTool.PROGRAM_MODE.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/UpgradeTo1_9_6.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentPositionComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadGroupHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionFacadeAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/FileSlice.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriterImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ExportableAlignmentEntryData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/Merge.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/DefaultAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NoUpgradeAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadIndexStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionBaseInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactoryBase.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/EntryFlagHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/RepositionableInputStream.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadOriginInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingSamBamWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentSliceHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractConcatAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/LastParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingAlignmentWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/GobyAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignedSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentToTextWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ScanReferenceSequence.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/HTSJdkReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ReferenceLocation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionToBasesMap.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatSortedAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/SamRecordGenomicPositionComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/GenomicRange.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/SortIterateAlignments.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractAlignmentReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReaderFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/class-use/HTSJDKReaderImpl.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/ObservedIndel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DefaultAlignmentProcessorFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/RealignmentProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToListIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/InfoForTarget.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyGenomeAlignmentTargetMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorFactory.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessorUnsorted.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToSortedReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/GenomeAlignmentTargetMapper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/LocalSortProcessor.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptBestScoreAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AlignmentQualityFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/AbstractAlignmentEntryFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreOnlyAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreAmbiguityAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/TranscriptsAlignmentFilter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/GeneTranscriptRelationships.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutationInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ConcatenatePermutations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReaderInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ReadNameToIndex.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/class-use/GobyVersion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.Result.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.AlternativeHypothesis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/config/class-use/GobyConfiguration.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/FastaParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/ReaderFastaParser.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BullardUpperQuartileNormalization.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SamplePair.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/EmpiricalPValueEstimator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/Log2FoldChangeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DataProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AlignedCountNormalization.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FDRAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/ChiSquareTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionResults.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderFromRegionsOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FormatFieldCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactRCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.ElementType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DummyObservationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/VCFWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BenjaminiHochbergAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionAnalysis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderTestSupport.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/CountRawSampleIdsCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/CountCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProvider.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/EstimatedTestDistributions.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/TTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/RpkmLikeNormalizationMethod.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BonferroniAdjustment.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SampleCountCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/TSVWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeNonZeroNonNaN.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AbstractOutputFormat.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MinCombinator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SampleStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactTestCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeMagnitudeCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/ElementIndexComparator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/NormalizationMethod.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/RegionWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AnnotationAveragingWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeDouble.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AverageCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AverageFisherRCalculator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeColumns.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
[WARNING] * Dequeues a document from the queue, returning an instance of {@link
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSite.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/PrintWeights.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/ReadsToText.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/DoInParallel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/SimulateBisulfiteReads.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/RenameWeights.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/FoldChangeForExonPairs.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/DumpTargetInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/MakeBisulfiteFastaExample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/TestSkipTo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/PlantIndels.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/class-use/GobyRuntimeException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/class-use/GobyException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/ConstantAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryPosition.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryAlignedLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorTargetAlignedLength.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorInsertSizes.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorPairFlags.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistancesToReadVariations.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/BasenameUtils.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorReadMappingQuality.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/CommitPropertiesStatAccumulator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToEndOfRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToStartOfRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorNumVariationsInRead.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorBaseQuality.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/xml/class-use/MethylStats.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/UnboundedFifoPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapCreator.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/GenomeDebugHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/WarningCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/CodecHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/LoggingOutputStream.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Timer.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/HeaderUtil.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/FileExtensionHelper.CompactFileType.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/OutputInfoFromWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/KnownIndelSet.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/VariantMapHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/AlignmentHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/IOUtil.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/SamSequenceVariation.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/IsDone.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Variant.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Variant.GobyIndelFromVCF.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/Variant.FromTo.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/SamHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/BaseToStringHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/LongNamedCounter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/LogIsConfigured.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/GrepReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/NamedCounters.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/StreamSignal.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/class-use/FromToFreq.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/class-use/CommitPropertyHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/ResettableObjectPoolInterface.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/Resettable.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/NullResettableObjectPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/class-use/QueueResettableObjectPool.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/class-use/SubSequenceMotifMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/class-use/MotifMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionRegistry.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/RegisterThis.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/class-use/DynamicOptionClient.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PostBarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/OverlapResult.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PreBarcodeMatcher.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcherResult.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec2.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/MoveToFrontCoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodecHelper.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/NotCompressedChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderPlus.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceBaseInfoCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastBufferedMessageChunksReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/NullChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/HybridChunkCodec1.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/ChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderOrder1.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/GZipChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/GzipOutputStreamWithCustomLevel.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/InvalidChecksumException.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksWriter.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/SequenceSegmentInfoCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksReader.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderOrder1.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderPlus.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderI.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoder.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/ProtobuffCollectionHandler.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/BZip2ChunkCodec.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/class-use/ParseReadsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/cli/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/compression/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/config/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/exception/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/stats/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/org/campagnelab/goby/xml/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/samples/package-use.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/overview-tree.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/deprecated-list.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/index.html...
[WARNING] Building index for all classes...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/allclasses-index.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/allpackages-index.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/index-all.html...
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
[WARNING] * Dequeues a document from the queue, returning an instance of {@link
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method.
[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<'
[WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<'
[WARNING] * Number of reads skipped because of sampleFraction value < 1.0d.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/search.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/overview-summary.html...
[WARNING] Generating /<<PKGBUILDDIR>>/goby-distribution/target/apidocs/help-doc.html...
[WARNING] 91 warnings
[INFO] Building jar: /<<PKGBUILDDIR>>/goby-distribution/target/goby-distribution-3.3.1-javadoc.jar
[INFO] 
[INFO] --- maven-assembly-plugin:3.4.2:single (make-assembly) @ goby-distribution ---
[INFO] Reading assembly descriptor: assembly/assembly.xml
[INFO] Building jar: /<<PKGBUILDDIR>>/goby-distribution/target/goby-bin.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Goby Framework 3.3.1:
[INFO] 
[INFO] Goby Framework ..................................... SUCCESS [  0.042 s]
[INFO] Goby I/O ........................................... SUCCESS [ 17.436 s]
[INFO] Goby Full Distribution ............................. SUCCESS [ 19.170 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  36.772 s
[INFO] Finished at: 2024-05-14T23:18:59Z
[INFO] ------------------------------------------------------------------------
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# Create a symlink to the directory with test data for tests run from the
# goby-distribution directory.
ln -s ../test-data goby-distribution/test-data
# The test-results directory should exist because test classes will write inside.
if [ ! -e test-results ]; then mkdir test-results/; fi
# Putting the JRI location in the path, as indicated in GobyRengine.java.
# Also indicating R_HOME, as found in http://rforge.net/JRI/.
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/R/site-library/rJava/jri" && \
        export R_HOME="/usr/lib/R" && \
        dh_auto_test --no-parallel
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode test
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
[WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16
[WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
[WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Goby Framework                                                     [pom]
[INFO] Goby I/O                                                           [jar]
[INFO] Goby Full Distribution                                             [jar]
[INFO] 
[INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
[INFO] Building Goby Framework 3.3.1                                      [1/3]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
[INFO] Building Goby I/O 3.3.1                                            [2/3]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The artifact org.apache.maven.plugins:maven-resources-plugin:jar:2.6 has been relocated to org.apache.maven.plugins:maven-resources-plugin:jar:3.3.0
[WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3
[INFO] 
[INFO] --- build-helper-maven-plugin:3.3.0:add-source (add-classes) @ goby-io ---
[INFO] Source directory: /<<PKGBUILDDIR>>/goby-io/target/generated-sources added.
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-java-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-io ---
[INFO] Copying 2 resources
[INFO] Copying 1 resource
[INFO] Copying 1 resource
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-io ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 260 source files to /<<PKGBUILDDIR>>/goby-io/target/classes
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /<<PKGBUILDDIR>>/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (default) @ goby-io ---
[WARNING] Parameter tasks is deprecated, use target instead
[INFO] Executing tasks
[INFO]      [copy] Copying 1 file to /<<PKGBUILDDIR>>
[INFO]      [copy] Copying 1 file to /<<PKGBUILDDIR>>/goby-io/target/classes
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ goby-io ---
[INFO] skip non existing resourceDirectory /<<PKGBUILDDIR>>/goby-io/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-io ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-io ---
[INFO] No tests to run.
[INFO] 
[INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
[INFO] Building Goby Full Distribution 3.3.1                              [3/3]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-distribution ---
[INFO] Copying 3 resources
[INFO] Copying 72 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-distribution ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 525 source files to /<<PKGBUILDDIR>>/goby-distribution/target/classes
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractCommandLineMode.java: Some input files use unchecked or unsafe operations.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractCommandLineMode.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ goby-distribution ---
[INFO] skip non existing resourceDirectory /<<PKGBUILDDIR>>/goby-distribution/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-distribution ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 120 source files to /<<PKGBUILDDIR>>/goby-distribution/target/test-classes
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Some input files use or override a deprecated API.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Recompile with -Xlint:deprecation for details.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestRealignmentProcessor.java: Some input files use unchecked or unsafe operations.
[INFO] /<<PKGBUILDDIR>>/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestRealignmentProcessor.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-distribution ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running TestSuite
original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT 
original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G 
original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT 
original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT 
Annotations loaded
Annotations loaded
Annotations loaded
Annotations loaded
Annotations loaded
count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3}
count keys [0, 3, 5, 11, 13]
-1 0.0
0 0.0
1 0.0
2 0.0
3 0.0
4 0.0
5 0.0
6 0.0
7 0.0
8 0.0
9 0.0
10 0.0
11 0.0
12 0.0
13 0.0
14 0.0
15 0.0
16 0.0
17 0.0
18 0.0
19 0.0
20 0.0
21 0.0
22 0.0
23 0.0
24 0.0
25 0.0
26 0.0
27 0.0
28 0.0
29 0.0
30 0.0
overlapping count 3, 4 0.0
overlapping count 15, 17 0.0
overlapping count 9, 18 2.0
overlapping count 3, 8 2.0
overlapping count 11, 12 0.0
overlapping count 9, 10 1.0
overlapping count 8, 9 0.0
overlapping count 8, 8 0.0
overlapping count 5, 6 0.0
overlapping count 3, 3 0.0
overlapping count 3, 12 5.0
overlapping count -1, 2 0.0
overlapping count 0, 45 6.0
overlapping count 13, 15 0.0
-1 0.0
0 0.0
1 0.0
2 0.0
3 2.0
4 2.0
5 3.0
6 3.0
7 3.0
8 3.0
9 3.0
10 3.0
11 2.0
12 2.0
13 0.0
14 0.0
15 1.0
16 1.0
17 1.0
18 1.0
19 0.0
20 0.0
21 0.0
22 0.0
23 0.0
24 0.0
25 0.0
26 0.0
27 0.0
28 0.0
29 0.0
30 0.0
overlapping count 3, 4 2.0
overlapping count 2, 3 2.0
overlapping count 3, 8 4.0
overlapping count 11, 12 2.0
overlapping count 9, 10 3.0
overlapping count 8, 9 4.0
overlapping count 8, 8 3.0
overlapping count 5, 6 3.0
overlapping count 3, 3 2.0
overlapping count 3, 12 5.0
overlapping count -1, 2 0.0
overlapping count 0, 45 6.0
overlapping count 13, 15 1.0
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/usr/share/java/slf4j-simple.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/<<PKGBUILDDIR>>/debian/maven-repo/ch/qos/logback/logback-classic/debian/logback-classic-debian.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/usr/share/java/logback-classic.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.SimpleLoggerFactory]
23:19:13.837 WARN  MessageChunksWriter - Using chunk-size=10000
Total logical entries written: 4
Total bytes written: 0
Average bytes/logical entry: 0.0
Min query index: 1
Max query index: 1
Number of queries: 1
Number of targets: 2
Total logical entries written: 4
Total bytes written: 62
Average bytes/logical entry: 15.5
Min query index: 1
Max query index: 1
Number of queries: 1
Number of targets: 2
23:19:13.875 WARN  GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent.
[main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 
[ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits
[ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 1
decoding: 2
decoding: 3
decoding: 4
decoding: 3
decoding: 1
decoding: 2
decoding: 1
decoding: 2
decoding: 3
decoding: 1
decoding: 2
decoding: 1
decoding: 2
decoding: 1
[ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits
[ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0
 {1} {0}decoding: 4
 {0} {0}decoding: 4
 {0} {0}decoding: 4
 {0}decoding: 4
 {0}decoding: 4
 {0}decoding: 4
decoding: 4
 {0}decoding: 4
 {0}decoding: 4
decoding: 4
 {0}decoding: 4
decoding: 4
 {0}decoding: 4
decoding: 4
 {0} {0} {0} {0} {0}decoding: 1
 {0} {0} {0} {0}decoding: 2
 {0} {0} {0} {0} {0}decoding: 3
decoding: 4
 {0} {0} {0} {0}decoding: 3
 {0} {0} {0}decoding: 1
 {0} {0} {0} {0}decoding: 2
 {0} {0} {0}decoding: 1
 {0} {0} {0}decoding: 2
 {0} {0} {0} {0}decoding: 3
 {0} {0} {0}decoding: 1
 {0} {0} {0}decoding: 2
 {0} {0}decoding: 1
 {0} {0} {0}decoding: 2
 {0} {0}decoding: 1
[ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits
[ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 4
decoding: 1
decoding: 2
decoding: 3
decoding: 4
decoding: 3
decoding: 1
decoding: 2
decoding: 1
decoding: 2
decoding: 3
decoding: 1
decoding: 2
decoding: 1
decoding: 2
decoding: 1
Total logical entries written: 1
Total bytes written: 0
Average bytes/logical entry: 0.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 45
field CHROM value: 0
field POS value: 145497099
field ID value: .
field REF value: A
field ALT value: G
field QUAL value: 17.1
field FILTER value: .
field INFO[DP] value: 2
field INFO[DP4] value: 0,0,2,0
field INFO[MQ] value: 25
field INFO[FQ] value: -30.8
field INFO[AF1] value: 0.9999
field INFO[CI95] value: 0.5,1
field INFO[PV4] value: 
field INFO[INDEL] value: INDEL
field INFO[PC2] value: 3,3
field INFO[PCHI2] value: 0.752
field INFO[QCHI2] value: 1
field INFO[RP] value: 
field FORMAT[GT] value: 
field FORMAT[GQ] value: 
field FORMAT[GL] value: 
field FORMAT[DP] value: 
field FORMAT[SP] value: 
field FORMAT[PL] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1
field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42
field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0
field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1
field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42
field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0
field CHROM gfi:0 value: 0
field POS gfi:1 value: 145497099
field ID gfi:2 value: .
field REF gfi:3 value: A
field ALT gfi:4 value: G
field QUAL gfi:5 value: 17.1
field FILTER gfi:6 value: .
field FORMAT[GT] gfi:7 value: 
field FORMAT[GQ] gfi:8 value: 
field FORMAT[GL] gfi:9 value: 
field FORMAT[DP] gfi:10 value: 
field FORMAT[SP] gfi:11 value: 
field FORMAT[PL] gfi:12 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1
field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11
field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0
field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1
field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42
field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0
 0 
AAC 3 
ACC 6 
ATC 9 
AGC 12 
AAC 15 
ACC 18 
ATC 21 
AGC 24 
AAC 27 
ACC 30 
ATC 33 
AGC 36 
AAC 39 
ACC 42 
ATC 45 
AGC 48 
AAC 51 
ACC 54 
ATC 57 
AGC 60 
AAC 63 
ACC 66 
ATC 69 
AGC 72 
AAC 75 
ACC 78 
ATC 81 
AGCqPhred=1
qPhred=2
qPhred=3
qPhred=4
qPhred=5
qPhred=6
qPhred=7
qPhred=8
qPhred=9
qPhred=10
qPhred=11
qPhred=12
qPhred=13
qPhred=14
qPhred=15
qPhred=16
qPhred=17
qPhred=18
qPhred=19
qPhred=20
qPhred=21
qPhred=22
qPhred=23
qPhred=24
qPhred=25
qPhred=26
qPhred=27
qPhred=28
qPhred=29
qPhred=30
qPhred=31
qPhred=32
qPhred=33
qPhred=34
qPhred=35
qPhred=36
qPhred=37
qPhred=38
qPhred=39
qPhred=40
qPhred=41
qPhred=42
qPhred=43
qPhred=44
qPhred=45
qPhred=46
qPhred=47
qPhred=48
qPhred=49
qPhred=50
qPhred=51
qPhred=52
qPhred=53
qPhred=54
qPhred=55
qPhred=56
qPhred=57
qPhred=58
qPhred=59
qPhred=60
qPhred=61
23:19:50.668 WARN  MessageChunksWriter - Using chunk-size=9
23:19:50.676 WARN  MessageChunksWriter - Using chunk-size=9
Total logical entries written: 39
Total bytes written: 660
Average bytes/logical entry: 16.923077
Number of bits/base 3.6590436
23:19:50.681 WARN  MessageChunksWriter - Using chunk-size=9
Total logical entries written: 39
Total bytes written: 685
Average bytes/logical entry: 17.564102
Number of bits/base 3.797644
23:19:50.686 WARN  MessageChunksWriter - Using chunk-size=9
Total logical entries written: 39
Total bytes written: 660
Average bytes/logical entry: 16.923077
Number of bits/base 3.6590436
>1
NNTGAATGAGACCTA

Scanning target file..
Target file had 1 entries.
Wrote 1 target ids to alignment header.
Setting quality threshold to 0.05
Total logical entries written: 2
Total bytes written: 0
Average bytes/logical entry: 0.0
Min query index: 0
Max query index: 0
Number of queries: 3
Number of targets: 3
Removed by quality filter: 0
Not best score: 1
Number of alignments written: 2
query_index: 0
target_index: 0
position: 14977972
score: 780.0
matching_reverse_strand: false
multiplicity: 1
number_of_mismatches: 1
number_of_indels: 0
query_length: 142
query_aligned_length: 134
target_aligned_length: 134
sequence_variations {
  to: "T"
  from: "A"
  position: 6
  to_quality: "/"
  read_index: 14
}
fragment_index: 0
query_index_occurrences: 2
ambiguity: 1

[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
                                               1/1 ..T

23:19:55.140 INFO  RLoggerMainLoopCallback - 

23:19:55.140 INFO  RLoggerMainLoopCallback - R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu


23:19:55.141 INFO  RLoggerMainLoopCallback - R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.


23:19:55.141 INFO  RLoggerMainLoopCallback - R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.


23:19:55.141 INFO  RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.


Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:55.482 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:55.484 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:55.485 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:55.486 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:55.487 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:55.488 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:55.489 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:55.490 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:55.491 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:55.492 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:55.579 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:55.582 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:55.584 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:55.586 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:55.588 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:55.591 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:55.594 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:55.598 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:55.599 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:55.600 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:55.648 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:55.649 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:55.650 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:55.651 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:55.652 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:55.653 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:55.654 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:55.655 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:55.656 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:55.656 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:55.700 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:55.701 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:55.702 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:55.703 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:55.704 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:55.705 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:55.705 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:55.706 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:55.707 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:55.708 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:55.768 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:55.768 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:55.769 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:55.770 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:55.772 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:55.773 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:55.774 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:55.776 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:55.778 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:55.780 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:55.826 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:55.826 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:55.827 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:55.828 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:55.829 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:55.829 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:55.830 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:55.831 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:55.832 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:55.833 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:55.876 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:55.877 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:55.877 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:55.878 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:55.879 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:55.880 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:55.881 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:55.882 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:55.883 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:55.883 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:55.921 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:55.922 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:55.923 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:55.924 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:55.925 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:55.926 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:55.927 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:55.927 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:55.928 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:55.929 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:55.967 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:55.968 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:55.969 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:55.970 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:55.970 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:55.971 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:55.972 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:55.973 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:55.973 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:55.974 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:56.013 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:56.015 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:56.016 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:56.017 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:56.018 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:56.018 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:56.019 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:56.020 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:56.021 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:56.022 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
Comparing A/B 
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Filtering reads that have these criteria:
q<30
#count(allele) < (2 *#filtered)
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:56.075 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:56.076 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:56.077 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:56.078 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:56.079 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:56.080 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:56.081 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:56.082 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:56.083 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:56.084 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
Associating basename: basen0 to group: A
Associating basename: basen1 to group: A
Associating basename: basen2 to group: A
Associating basename: basen3 to group: A
Associating basename: basen4 to group: A
Associating basename: basen5 to group: B
Associating basename: basen6 to group: B
Associating basename: basen7 to group: B
Associating basename: basen8 to group: B
Associating basename: basen9 to group: B
sample: basen0 group A
sample: basen2 group A
sample: basen4 group A
sample: basen3 group A
sample: basen1 group A
sample: basen9 group B
sample: basen6 group B
sample: basen5 group B
sample: basen7 group B
sample: basen8 group B
Using processor NONE
Methylation format ignores thresholdDistinctReadIndices. Additionally, the minimum coverage needed for a site to be reported can be changed with --minimum-variation-support.
Filtering reads that have these criteria:
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest_mci
[main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0
[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
23:19:56.138 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0
23:19:56.139 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1
23:19:56.140 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2
23:19:56.141 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3
23:19:56.142 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4
23:19:56.143 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5
23:19:56.144 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6
23:19:56.145 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7
23:19:56.147 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8
23:19:56.148 INFO  AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9
info: + ref: A s=0
info: + ref: A s=0
info: + ref: A s=0
info: + ref: A s=0
info: + ref: A s=0
info: +  /T q=40 s=0
info: -  /T q=40 s=0
info: +  /C q=10 s=0
info: +  /C q=20 s=0
info: +  /C q=30 s=0
info: +  /C q=40 s=0
info: +  /C q=40 s=0
info: +  /C q=40 s=0
info: +  /C q=40 s=0
info: +  /C q=10 s=0
info: +  /C q=20 s=0
info: +  /N q=30 s=0
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: + ref: A s=1
info: +  /T q=40 s=1
info: +  /T q=10 s=1
info: +  /T q=20 s=1
info: +  /T q=30 s=1
info: +  /N q=40 s=1
info: +  /N q=40 s=1
list: pos=-1 #bases: 33 #indels: 0
filtered: {+ ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, +  /C q=10 s=0, +  /C q=20 s=0, +  /C q=30 s=0, +  /C q=40 s=0, +  /C q=40 s=0, +  /C q=40 s=0, +  /C q=40 s=0, +  /C q=10 s=0, +  /C q=20 s=0, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, +  /T q=40 s=1, +  /T q=10 s=1, +  /T q=20 s=1, +  /T q=30 s=1, +  /N q=40 s=1, +  /N q=40 s=1}
TTC[27]->CGT[27] / qual=1:2:3
A[15]->G[20] / qual=20
A[15]->G[20] / qual=20
Loading test-data/fdr-mode/file1.vcf
Loading test-data/fdr-mode/file2.vcf
Loading test-data/fdr-mode/file3.vcf
adjusting column: PCHI2
Combining test-data/fdr-mode/file1.vcf
Combining test-data/fdr-mode/file2.vcf
Combining test-data/fdr-mode/file3.vcf
Loading test-data/fdr-mode/file-B-1.vcf
Loading test-data/fdr-mode/file-B-2.vcf
adjusting column: PCHI2
Combining test-data/fdr-mode/file-B-1.vcf
Combining test-data/fdr-mode/file-B-2.vcf
Loading test-data/fdr-mode/file-B-1.vcf
Loading test-data/fdr-mode/file-B-2.vcf
adjusting column: PCHI2
Combining test-data/fdr-mode/file-B-1.vcf
Combining test-data/fdr-mode/file-B-2.vcf
Loading test-data/fdr-mode/file1.vcf
Loading test-data/fdr-mode/file2.vcf
Loading test-data/fdr-mode/file3.vcf
Combining test-data/fdr-mode/file1.vcf
Combining test-data/fdr-mode/file2.vcf
Combining test-data/fdr-mode/file3.vcf
Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads
Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads
Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads
Processing test-data/sample-qual-scores/30reads.fa
Processed 0 read entries.
Min quality score: 2147483647
Max quality score: -2147483648
Avg quality score: 0
Probable quality encoding scheme: fasta
Processing test-data/sample-qual-scores/30reads.fq
Processed 30 read entries.
Min quality score: 69
Max quality score: 98
Avg quality score: 94
Probable quality encoding scheme: Illumina/Solexa
Appending count: 13616 length: 3
Appending count: 909 length: 6
Appending count: 5913 length: 5
Appending count: 46777 length: 3
Appending count: 33278 length: 5
Appending count: 38653 length: 6
Appending count: 15355 length: 9
Appending count: 17826 length: 8
Appending count: 40311 length: 5
Appending count: 47610 length: 9
Appending count: 36398 length: 4
Appending count: 32566 length: 1
Appending count: 6729 length: 6
Appending count: 15733 length: 3
Appending count: 8664 length: 9
Appending count: 7670 length: 9
Appending count: 21553 length: 9
Appending count: 32494 length: 4
Appending count: 6754 length: 8
Appending count: 39221 length: 7
Appending count: 17251 length: 8
Appending count: 5899 length: 1
Appending count: 22631 length: 7
Appending count: 48984 length: 1
Appending count: 23473 length: 9
Appending count: 28113 length: 9
Appending count: 25972 length: 4
Appending count: 43831 length: 3
Appending count: 1602 length: 9
Appending count: 40809 length: 4
 position= 0 count= 13616
 position= 1 count= 13616
 position= 2 count= 13616
 position= 3 count= 909
 position= 4 count= 909
 position= 5 count= 909
 position= 6 count= 909
 position= 7 count= 909
 position= 8 count= 909
 position= 9 count= 5913
 position= 10 count= 5913
 position= 11 count= 5913
 position= 12 count= 5913
 position= 13 count= 5913
 position= 14 count= 46777
 position= 15 count= 46777
 position= 16 count= 46777
 position= 17 count= 33278
 position= 18 count= 33278
 position= 19 count= 33278
 position= 20 count= 33278
 position= 21 count= 33278
 position= 22 count= 38653
 position= 23 count= 38653
 position= 24 count= 38653
 position= 25 count= 38653
 position= 26 count= 38653
 position= 27 count= 38653
 position= 28 count= 15355
 position= 29 count= 15355
 position= 30 count= 15355
 position= 31 count= 15355
 position= 32 count= 15355
 position= 33 count= 15355
 position= 34 count= 15355
 position= 35 count= 15355
 position= 36 count= 15355
 position= 37 count= 17826
 position= 38 count= 17826
 position= 39 count= 17826
 position= 40 count= 17826
 position= 41 count= 17826
 position= 42 count= 17826
 position= 43 count= 17826
 position= 44 count= 17826
 position= 45 count= 40311
 position= 46 count= 40311
 position= 47 count= 40311
 position= 48 count= 40311
 position= 49 count= 40311
 position= 50 count= 47610
 position= 51 count= 47610
 position= 52 count= 47610
 position= 53 count= 47610
 position= 54 count= 47610
 position= 55 count= 47610
 position= 56 count= 47610
 position= 57 count= 47610
 position= 58 count= 47610
 position= 59 count= 36398
 position= 60 count= 36398
 position= 61 count= 36398
 position= 62 count= 36398
 position= 63 count= 32566
 position= 64 count= 6729
 position= 65 count= 6729
 position= 66 count= 6729
 position= 67 count= 6729
 position= 68 count= 6729
 position= 69 count= 6729
 position= 70 count= 15733
 position= 71 count= 15733
 position= 72 count= 15733
 position= 73 count= 8664
 position= 74 count= 8664
 position= 75 count= 8664
 position= 76 count= 8664
 position= 77 count= 8664
 position= 78 count= 8664
 position= 79 count= 8664
 position= 80 count= 8664
 position= 81 count= 8664
 position= 82 count= 7670
 position= 83 count= 7670
 position= 84 count= 7670
 position= 85 count= 7670
 position= 86 count= 7670
 position= 87 count= 7670
 position= 88 count= 7670
 position= 89 count= 7670
 position= 90 count= 7670
 position= 91 count= 21553
 position= 92 count= 21553
 position= 93 count= 21553
 position= 94 count= 21553
 position= 95 count= 21553
 position= 96 count= 21553
 position= 97 count= 21553
 position= 98 count= 21553
 position= 99 count= 21553
 position= 100 count= 32494
 position= 101 count= 32494
 position= 102 count= 32494
 position= 103 count= 32494
 position= 104 count= 6754
 position= 105 count= 6754
 position= 106 count= 6754
 position= 107 count= 6754
 position= 108 count= 6754
 position= 109 count= 6754
 position= 110 count= 6754
 position= 111 count= 6754
 position= 112 count= 39221
 position= 113 count= 39221
 position= 114 count= 39221
 position= 115 count= 39221
 position= 116 count= 39221
 position= 117 count= 39221
 position= 118 count= 39221
 position= 119 count= 17251
 position= 120 count= 17251
 position= 121 count= 17251
 position= 122 count= 17251
 position= 123 count= 17251
 position= 124 count= 17251
 position= 125 count= 17251
 position= 126 count= 17251
 position= 127 count= 5899
 position= 128 count= 22631
 position= 129 count= 22631
 position= 130 count= 22631
 position= 131 count= 22631
 position= 132 count= 22631
 position= 133 count= 22631
 position= 134 count= 22631
 position= 135 count= 48984
 position= 136 count= 23473
 position= 137 count= 23473
 position= 138 count= 23473
 position= 139 count= 23473
 position= 140 count= 23473
 position= 141 count= 23473
 position= 142 count= 23473
 position= 143 count= 23473
 position= 144 count= 23473
 position= 145 count= 28113
 position= 146 count= 28113
 position= 147 count= 28113
 position= 148 count= 28113
 position= 149 count= 28113
 position= 150 count= 28113
 position= 151 count= 28113
 position= 152 count= 28113
 position= 153 count= 28113
 position= 154 count= 25972
 position= 155 count= 25972
 position= 156 count= 25972
 position= 157 count= 25972
 position= 158 count= 43831
 position= 159 count= 43831
 position= 160 count= 43831
 position= 161 count= 1602
 position= 162 count= 1602
 position= 163 count= 1602
 position= 164 count= 1602
 position= 165 count= 1602
 position= 166 count= 1602
 position= 167 count= 1602
 position= 168 count= 1602
 position= 169 count= 1602
 position= 170 count= 40809
 position= 171 count= 40809
 position= 172 count= 40809
 position= 173 count= 40809
 peak : start :5 count :13 length :100010
 peak : start :100020 count :10 length :1
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=6 count=1 
(0,1)
loading transition for reader[0] position=1 length=3 count=3 
(0,1)(1,4)
loading transition for reader[0] position=4 length=2 count=0 
(0,1)(1,4)(4,1)
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=4 count=0 
(0,0)
loading transition for reader[0] position=1 length=1 count=1 
(0,0)(1,1)
loading transition for reader[0] position=2 length=4 count=0 
(0,0)(1,1)(2,0)
loading transition for reader[1] position=4 length=10 count=1 
(0,0)(1,1)(2,0)(4,1)
loading transition for reader[0] position=6 length=2 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)
loading transition for reader[0] position=8 length=1 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)
loading transition for reader[0] position=9 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)
loading transition for reader[0] position=10 length=2 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)
loading transition for reader[0] position=12 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)
loading transition for reader[0] position=13 length=3 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)
loading transition for reader[0] position=16 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1)
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=4 count=0 
loading transition for reader[0] position=1 length=1 count=1 
loading transition for reader[0] position=2 length=4 count=0 
loading transition for reader[1] position=4 length=10 count=1 
loading transition for reader[0] position=6 length=2 count=1 
loading transition for reader[0] position=8 length=1 count=0 
loading transition for reader[0] position=9 length=1 count=1 
loading transition for reader[0] position=10 length=2 count=0 
loading transition for reader[0] position=12 length=1 count=1 
loading transition for reader[0] position=13 length=3 count=0 
loading transition for reader[0] position=16 length=1 count=1 
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=6 count=1 
(0,1)
loading transition for reader[0] position=1 length=3 count=3 
(0,1)(1,4)
loading transition for reader[0] position=4 length=2 count=0 
(0,1)(1,4)(4,1)
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=4 count=0 
(0,0)
loading transition for reader[0] position=1 length=1 count=1 
(0,0)(1,1)
loading transition for reader[0] position=2 length=4 count=0 
(0,0)(1,1)(2,0)
loading transition for reader[1] position=4 length=10 count=1 
(0,0)(1,1)(2,0)(4,1)
loading transition for reader[0] position=6 length=2 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)
loading transition for reader[0] position=8 length=1 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)
loading transition for reader[0] position=9 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)
loading transition for reader[0] position=10 length=2 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)
loading transition for reader[0] position=12 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)
loading transition for reader[0] position=13 length=3 count=0 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)
loading transition for reader[0] position=16 length=1 count=1 
(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1)
loading transition for reader[0] position=0 length=1 count=0 
loading transition for reader[1] position=0 length=4 count=0 
loading transition for reader[0] position=1 length=1 count=1 
loading transition for reader[0] position=2 length=4 count=0 
loading transition for reader[1] position=4 length=10 count=1 
loading transition for reader[0] position=6 length=2 count=1 
loading transition for reader[0] position=8 length=1 count=0 
loading transition for reader[0] position=9 length=1 count=1 
loading transition for reader[0] position=10 length=2 count=0 
loading transition for reader[0] position=12 length=1 count=1 
loading transition for reader[0] position=13 length=3 count=0 
loading transition for reader[0] position=16 length=1 count=1 
loading transition for reader[0] position=0 length=1 count=0 
(0,0)
loading transition for reader[0] position=1 length=3 count=1 
(0,0)(1,1)
 appending (count=0,length=1)
 appending (count=4,length=3)
 appending (count=1,length=3)
 appending (count=0,length=2)
 appending (count=3,length=1)
 appending (count=1,length=1)
 appending (count=0,length=1)
 appending (count=4,length=3)
 appending (count=0,length=5)
 appending (count=3,length=1)
 appending (count=0,length=2)
 appending (count=2,length=1)
 appending (count=0,length=2)
 appending (count=3,length=1)
 appending (count=2,length=1)
 appending (count=0,length=1)
23:19:56.975 WARN  WiggleWindow - Not writing 101 7
23:19:56.975 WARN  WiggleWindow - Not writing 111 7
23:19:56.975 WARN  WiggleWindow - Not writing 131 8
23:19:56.975 WARN  WiggleWindow - Not writing 141 8
23:19:56.976 WARN  WiggleWindow - Not writing 151 8
 appending (count=10,length=4)
 appending (count=1,length=0)
 appending (count=2,length=8)
Hello
 appending (count=10,length=4)
23:19:56.977 WARN  MessageChunksWriter - Using chunk-size=1000

23:19:56.984 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 0
Total bytes written: 31
Average bytes/logical entry: Infinity
Min query index: 2147483647
Max query index: -2147483648
Number of queries: 2
Number of targets: 0
97
23:19:56.987 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
23:19:56.991 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
23:19:56.993 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
23:19:56.994 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
23:19:56.999 WARN  MessageChunksWriter - Using chunk-size=1000
Total logical entries written: 20000
Total bytes written: 77210
Average bytes/logical entry: 3.8605
Min query index: 0
Max query index: 1999
Number of queries: 2000
Number of targets: 10
entry:query_index: 0
target_index: 0
position: 5
score: 5.0
matching_reverse_strand: false
query_length: 20
query_aligned_length: 20
target_aligned_length: 20
sequence_variations {
  to: "CTAG"
  from: "----"
  position: 10
  read_index: 10
}

entry:query_index: 1
target_index: 0
position: 5
matching_reverse_strand: false
query_length: 20
query_aligned_length: 20
target_aligned_length: 20
sequence_variations {
  to: "CTAG"
  from: "----"
  position: 10
  to_quality: "(((("
  read_index: 10
}

entry: query_index: 0
target_index: 0
position: 0
matching_reverse_strand: false
query_length: 10
query_aligned_length: 10
sequence_variations {
  to: "AAA"
  from: "---"
  position: 3
  read_index: 3
}

processing entry on target 0 at position 0 
processing entry on target 0 at position 5 
processing entry on target 1 at position 0 
processing entry on target 1 at position 5 
processing entry on target 4 at position 0 
processing entry on target 4 at position 5 
entry:query_index: 0
target_index: 0
position: 10
matching_reverse_strand: false
query_length: 50
query_aligned_length: 50
sequence_variations {
  to: "AAA"
  from: "---"
  position: 20
  read_index: 20
}

entry:query_index: 1
target_index: 0
position: 1
matching_reverse_strand: false
query_length: 50
query_aligned_length: 50
sequence_variations {
  to: "T"
  from: "A"
  position: 20
  read_index: 20
}

query_index: 0
target_index: 0
position: 0
query_position: 0
matching_reverse_strand: false
query_length: 75
query_aligned_length: 75
target_aligned_length: 75
mapping_quality: 255
pair_flags: 0
fragment_index: 0
ambiguity: 1

query_index: 1
target_index: 0
position: 1
query_position: 0
matching_reverse_strand: false
query_length: 75
query_aligned_length: 75
target_aligned_length: 75
mapping_quality: 255
pair_flags: 0
fragment_index: 0
ambiguity: 1

23:19:57.072 WARN  MessageChunksWriter - Using chunk-size=1
23:19:57.075 WARN  MessageChunksWriter - Using chunk-size=1
23:19:57.077 WARN  MessageChunksWriter - Using chunk-size=1
23:19:57.079 WARN  MessageChunksWriter - Using chunk-size=1
23:19:57.091 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.121 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.122 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.151 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
23:19:57.177 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.178 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.183 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.202 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.202 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
23:19:57.202 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ∞ items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 250.06M/3.94G/45.64M/295.70M/4.19G
23:19:57.208 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
found entry: query_index: 0
target_index: 1999
position: 19991
score: 20020.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 1999
position: 19992
score: 20021.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

23:19:57.235 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.239 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.276 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.276 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.276 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.276 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
23:19:57.276 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.276 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 61.57M/4.13G/148.15M/209.72M/4.19G
23:19:57.280 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.293 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.315 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.341 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.342 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.365 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
23:19:57.388 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.389 WARN  MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]; used/avail/free/total/max mem: 85.37M/4.11G/124.34M/209.72M/4.19G
found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 3999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 3999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 3999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 3999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 3999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 3999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 3999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 3999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

23:19:57.444 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.464 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.465 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.486 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
23:19:57.507 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.508 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.509 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.513 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.513 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
23:19:57.513 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ∞ items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 144.08M/4.05G/65.64M/209.72M/4.19G
23:19:57.514 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
notBestScoreCount=16.6667 % geneAmbiguityCount=33.3333 % 
found entry: query_index: 0
target_index: 1
position: 2
score: 31.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 0
target_index: 2
position: 3
score: 31.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 4
position: 6
score: 30.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

23:19:57.517 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.538 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.540 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.564 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
23:19:57.585 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.585 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.587 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
23:19:57.588 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
23:19:57.589 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
23:19:57.589 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
23:19:57.589 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
23:19:57.589 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
23:19:57.590 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
23:19:57.590 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 44.39M/4.15G/236.63M/281.02M/4.19G
23:19:57.591 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
23:19:57.592 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
23:19:57.594 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.615 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.616 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.638 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
23:19:57.660 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.661 WARN  MessageChunksWriter - Using chunk-size=1000
Finding max number of reads...
Found input file with 2 target(s)
23:19:57.662 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
Found input file with 2 target(s)
23:19:57.663 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
... max number of reads was 10
First pass: determine which reads should be kept in the merged alignment.
Scanning align-105
Scanning align-106
Found 40 logical alignment entries.
Prepare merged too many hits information.
23:19:57.664 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
23:19:57.664 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
23:19:57.665 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
23:19:57.665 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
23:19:57.665 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
23:19:57.665 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 70.60M/4.12G/210.42M/281.02M/4.19G
Second pass: writing the merged alignment.
23:19:57.666 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
23:19:57.667 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits.
Wrote 20  skipped: 20 50.000000% too many hits 0.000000% notBestScore: 50.000000%
Total logical entries written: 20
Total bytes written: 0
Average bytes/logical entry: 0.0
Min query index: 0
Max query index: 9
Number of queries: 10
Number of targets: 4
Percent aligned: 100.0
23:19:57.669 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.691 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.693 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.716 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
23:19:57.737 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.738 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.739 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
23:19:57.740 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
23:19:57.740 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
23:19:57.740 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ∞ items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 95.77M/4.10G/185.25M/281.02M/4.19G
23:19:57.741 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits.
found entry: query_index: 0
target_index: 1
position: 11
score: 40.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 1
position: 12
score: 41.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 1
position: 13
score: 42.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1
position: 14
score: 43.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1
position: 15
score: 44.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1
position: 16
score: 45.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1
position: 17
score: 46.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1
position: 18
score: 47.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1
position: 19
score: 48.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1
position: 20
score: 49.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

23:19:57.744 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.766 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.767 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.789 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
23:19:57.811 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.812 WARN  MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 µs/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]; used/avail/free/total/max mem: 153.44M/4.04G/127.58M/281.02M/4.19G
found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 3999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 3999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 3999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 3999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 3999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 3999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 3999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 3999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

23:19:57.888 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.914 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.915 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.943 WARN  MessageChunksWriter - Using chunk-size=1000
preparing 105
23:19:57.967 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.968 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:57.971 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.974 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.995 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.995 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.995 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.995 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
23:19:57.995 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:57.995 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ∞ items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 78.85M/4.12G/202.17M/281.02M/4.19G
23:19:57.997 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
23:19:58.009 INFO  AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits.
found entry: query_index: 0
target_index: 1999
position: 19991
score: 20020.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 1999
position: 19992
score: 20021.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 0
target_index: 3999
position: 19991
score: 20020.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 3999
position: 19992
score: 20021.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 3999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 3999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 3999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 3999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 3999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 3999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 3999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 3999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

read       =CTCCAGAACTGTAAGATAATAAGTTGGTGTTGTTTT
expected   =TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT
recons. ref=TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT
read       =TTTCCCACATTTCCCATCACCACTACTACGGATACAGAACGGGG
expected   =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
read       =TTTCCCAAATTTCACATCACTACTACACGGATACAGAACGGGG
expected   =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
read       =TAAAACCTAAAAAAAAAAAAAAACCCC
expected   =TAAAA--TAAAAAAAAAAAAAAACCCC
recons. ref=TAAAA--TAAAAAAAAAAAAAAACCCC
read       =TTTTGATGAAGTCTCTGTGTCCTGGGGCATCAATGATGGTCACA
expected   =TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA
recons. ref=TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA
read       =TTTCCCAAATTTCACATCACTACACTACGGATACAGAACGGGG
expected   =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG
read       =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT
expected   =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT
recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT
23:19:58.038 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.039 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.039 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.043 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.044 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.045 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.048 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.049 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.050 WARN  MessageChunksWriter - Using chunk-size=1000
entry.position(): 1
entry.position(): 2
entry.position(): 3
entry.position(): 5
entry.position(): 6
entry.position(): 7
entry.position(): 8
entry.position(): 9
entry.position(): 10
entry.position(): 10
entry.position(): 12
entry.position(): 99
23:19:58.054 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.055 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.056 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.061 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.063 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.063 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.065 INFO  AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-1.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-1.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-1
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-1
23:19:58.065 INFO  AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-2.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-2.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-2
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-2
23:19:58.066 INFO  AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-3.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-3.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-3
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-3
23:19:58.068 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.069 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.069 WARN  MessageChunksWriter - Using chunk-size=1000
Processing queryIndex=8 with description '8 perfect start of ref'
Processing queryIndex=9 with description '9 perfect start of ref reverse strand'
Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1'
Processing queryIndex=19 with description '19 mismatch at end x2, starting at -1'
Processing queryIndex=20 with description '20 mismatch at end x5, starting at -1'
Processing queryIndex=21 with description '21 mismatch at end x1, starting at -2'
Processing queryIndex=22 with description '22 mismatch at end x2, starting at -2'
Processing queryIndex=23 with description '23 mismatch at end x5, starting at -2'
Processing queryIndex=12 with description '12 mismatch at beginning x1, starting at 1, with mutation at 20'
Processing queryIndex=13 with description '13 mismatch at beginning x2, starting at 1, with mutation at 20'
Processing queryIndex=15 with description '15 mismatch at beginning x1, starting at 2'
Processing queryIndex=16 with description '16 mismatch at beginning x2, starting at 2'
Processing queryIndex=14 with description '14 mismatch at beginning x5, starting at 1 (pos 4 actually does match), with mutation at 20'
Processing queryIndex=17 with description '17 mismatch at beginning x5, starting at 2 (pos 4 actually does match)'
Processing queryIndex=0 with description '0  perfect match'
Processing queryIndex=1 with description '1  perfect match on reverse strand'
Processing queryIndex=2 with description '2  mutation'
Processing queryIndex=3 with description '3  mutation on reverse strand'
Processing queryIndex=4 with description '4  insertion'
Processing queryIndex=6 with description '6  deletion'
Processing queryIndex=7 with description '7  deletion on reverse strand'
Processing queryIndex=27 with description '27 padding left & right, deletion then mutation'
Processing queryIndex=24 with description '24 padding left & right, mutation, deletion'
Processing queryIndex=5 with description '5  insertion on reverse strand'
Processing queryIndex=10 with description '10 perfect end of ref'
Processing queryIndex=11 with description '11 perfect end of ref reverse strand'
Setting quality threshold to 0.02
23:19:58.090 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
23:19:58.092 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
23:19:58.094 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
23:19:58.095 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
23:19:58.098 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
23:19:58.101 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
23:19:58.105 WARN  MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
23:19:58.110 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.113 WARN  MessageChunksWriter - Using chunk-size=1000
entry: score=30.0000 readOriginIndex=0 
entry: score=30.0000 readOriginIndex=0 
entry: score=50.0000 readOriginIndex=3 
entry: score=50.0000 readOriginIndex=3 
entry: score=50.0000 readOriginIndex=3 
Scanned 5 entries
23:19:58.121 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.123 WARN  MessageChunksWriter - Using chunk-size=1000
entry: score=30.0000 readOriginIndex=0 
entry: score=30.0000 readOriginIndex=0 
Scanned 2 entries
23:19:58.132 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.134 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.138 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.139 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.143 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.145 WARN  MessageChunksWriter - Using chunk-size=1000
0
2
23:19:58.150 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.151 WARN  MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-101
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-101
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-102
[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-102
23:19:58.156 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.157 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.161 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.162 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.166 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.167 WARN  MessageChunksWriter - Using chunk-size=1000
entry: score=50.0000 readOriginIndex=3 
entry: score=50.0000 readOriginIndex=3 
entry: score=50.0000 readOriginIndex=3 
entry: score=30.0000 readOriginIndex=0 
entry: score=30.0000 readOriginIndex=0 
Scanned 5 entries
23:19:58.173 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.177 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.183 WARN  MessageChunksWriter - Using chunk-size=1000
23:19:58.185 WARN  MessageChunksWriter - Using chunk-size=1000
0
23
[main] WARN org.campagnelab.goby.alignments.BufferedSortingAlignmentWriter - Local sorting strategy failed to restore sort order. The destination has been marked as unsorted. You must sort the output manually to improve compression.
23:19:58.292 INFO  FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value
23:19:58.335 INFO  FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed.
23:19:58.335 INFO  FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value
23:19:58.386 INFO  FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed.
23:19:58.387 INFO  FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value
23:19:58.496 INFO  FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed.
23:19:58.520 INFO  FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed.
23:19:58.520 INFO  FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value
23:19:58.610 INFO  FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed.
23:19:58.629 INFO  FDRAdjustment - ... statistic another-p-value-Bonferroni-adjusted was found, FDR adjustment executed.
list3:element-id p-value p-value-BH-FDR-q-value 
[ 0 [2.354054E-7, 1.177027E-5] ]
[ 1 [2.10159E-5, 4.294736666666667E-4] ]
[ 2 [2.576842E-5, 4.294736666666667E-4] ]
[ 3 [9.814783E-5, 9.471342857142858E-4] ]
[ 4 [1.05261E-4, 9.471342857142858E-4] ]
[ 5 [1.241481E-4, 9.471342857142858E-4] ]
[ 6 [1.325988E-4, 9.471342857142858E-4] ]
[ 7 [1.568503E-4, 9.803143750000002E-4] ]
[ 8 [2.254557E-4, 0.0012525316666666666] ]
[ 9 [3.79538E-4, 0.00189769] ]
[ 10 [6.114943E-4, 0.0027795195454545455] ]
[ 11 [0.001613954, 0.006724808333333334] ]
[ 12 [0.00330243, 0.012636935714285714] ]
[ 13 [0.003538342, 0.012636935714285714] ]
[ 14 [0.005236997, 0.017456656666666667] ]
[ 15 [0.006831909, 0.020762429411764708] ]
[ 16 [0.007059226, 0.020762429411764708] ]
[ 17 [0.008805129, 0.024458691666666667] ]
[ 18 [0.00940104, 0.02473957894736842] ]
[ 19 [0.01129798, 0.028244949999999998] ]
[ 20 [0.02115017, 0.050357547619047614] ]
[ 21 [0.04922736, 0.11188036363636364] ]
[ 22 [0.06053298, 0.1304633125] ]
[ 23 [0.06262239, 0.1304633125] ]
[ 24 [0.07395153, 0.14790306] ]
[ 25 [0.08281103, 0.15925198076923075] ]
[ 26 [0.08633331, 0.1598765] ]
[ 27 [0.1190654, 0.21261678571428572] ]
[ 28 [0.1890796, 0.32599931034482754] ]
[ 29 [0.2058494, 0.3430823333333333] ]
[ 30 [0.2209214, 0.3563248387096774] ]
[ 31 [0.2856, 0.44625000000000004] ]
[ 32 [0.3048895, 0.4619537878787878] ]
[ 33 [0.4660682, 0.6835770833333333] ]
[ 34 [0.4830809, 0.6835770833333333] ]
[ 35 [0.4921755, 0.6835770833333333] ]
[ 36 [0.5319453, 0.718845] ]
[ 37 [0.575155, 0.7414352564102564] ]
[ 38 [0.5783195, 0.7414352564102564] ]
[ 39 [0.6185894, 0.7626062790697675] ]
[ 40 [0.636362, 0.7626062790697675] ]
[ 41 [0.6448587, 0.7626062790697675] ]
[ 42 [0.6558414, 0.7626062790697675] ]
[ 43 [0.6885884, 0.7824868181818182] ]
[ 44 [0.7189864, 0.7988737777777778] ]
[ 45 [0.8179539, 0.8802645744680851] ]
[ 46 [0.8274487, 0.8802645744680851] ]
[ 47 [0.89713, 0.9304775510204082] ]
[ 48 [0.911868, 0.9304775510204082] ]
[ 49 [0.943789, 0.943789] ]

element-id average RPKM group A(AC) average RPKM group B(AC) average log2_RPKM group A(AC) average log2_RPKM group B(AC) average count group A average count group B 
[ id-1 [0.9992804047446895, 0.5006698198018502, -0.0010385302118203748, -0.9980686019871445, 0.0, 0.0] ]

truncated fdr=3.53108e-05 original=3.53108e-05 
truncated fdr=0.00128842 original=0.00128842 
truncated fdr=0.00128842 original=0.00128842 
truncated fdr=0.00284140 original=0.00284140 
truncated fdr=0.00284140 original=0.00284140 
truncated fdr=0.00284140 original=0.00284140 
truncated fdr=0.00284140 original=0.00284140 
truncated fdr=0.00294094 original=0.00294094 
truncated fdr=0.00375760 original=0.00375760 
truncated fdr=0.00569307 original=0.00569307 
truncated fdr=0.00833856 original=0.00833856 
truncated fdr=0.0201744 original=0.0201744 
truncated fdr=0.0379108 original=0.0379108 
truncated fdr=0.0379108 original=0.0379108 
truncated fdr=0.0523700 original=0.0523700 
truncated fdr=0.0622873 original=0.0622873 
truncated fdr=0.0622873 original=0.0622873 
truncated fdr=0.0733761 original=0.0733761 
truncated fdr=0.0742187 original=0.0742187 
truncated fdr=0.0847349 original=0.0847349 
truncated fdr=0.151073 original=0.151073 
truncated fdr=0.335641 original=0.335641 
truncated fdr=0.391390 original=0.391390 
truncated fdr=0.391390 original=0.391390 
truncated fdr=0.443709 original=0.443709 
truncated fdr=0.477756 original=0.477756 
truncated fdr=0.479630 original=0.479630 
truncated fdr=0.637850 original=0.637850 
truncated fdr=0.977998 original=0.977998 
truncated fdr=1.00000 original=1.00000 
truncated fdr=1.00000 original=1.00000 
truncated fdr=1.00000 original=1.00000 
truncated fdr=1.00000 original=1.00000 
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 4 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 4 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 4 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 4 threads.
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 42787.2 for sample B-7
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 43018.5 for sample B-3
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 88870.2 for sample A-3
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 89910.9 for sample A-12
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 43249.8 for sample B-15
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 42960.7 for sample B-14
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 43712.3 for sample B-11
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 87482.5 for sample A-17
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 43828.0 for sample B-2
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 44001.4 for sample B-10
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 85690.0 for sample A-16
23:20:11.254 INFO  BullardUpperQuartileNormalization - normalization denominator 43134.1 for sample B-8
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 43191.9 for sample B-4
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 84880.6 for sample A-2
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 87829.4 for sample A-0
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 41283.9 for sample B-6
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 86557.4 for sample A-9
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 86152.6 for sample A-8
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 87193.4 for sample A-5
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 86152.6 for sample A-4
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 86441.7 for sample A-6
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 88349.8 for sample A-7
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 43538.9 for sample B-5
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 87713.8 for sample A-10
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 88696.7 for sample A-14
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 43249.8 for sample B-9
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 85054.0 for sample A-1
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 43249.8 for sample B-0
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 43249.8 for sample B-12
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 43249.8 for sample B-13
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 85632.2 for sample A-19
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 87655.9 for sample A-18
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 84938.4 for sample A-15
23:20:11.255 INFO  BullardUpperQuartileNormalization - normalization denominator 43018.5 for sample B-1
23:20:11.256 INFO  BullardUpperQuartileNormalization - normalization denominator 86904.3 for sample A-13
23:20:11.256 INFO  BullardUpperQuartileNormalization - normalization denominator 85690.0 for sample A-11
23:20:11.256 INFO  BullardUpperQuartileNormalization - normalization denominator 42729.4 for sample B-16
23:20:11.256 INFO  BullardUpperQuartileNormalization - normalization denominator 42266.8 for sample B-17
23:20:11.256 INFO  BullardUpperQuartileNormalization - normalization denominator 42729.4 for sample B-19
23:20:11.256 INFO  BullardUpperQuartileNormalization - normalization denominator 44579.6 for sample B-18
Creating base test directory: test-results/stats
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG]
[main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest
[main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded.
##fileformat=VCFv4.1
##Goby=UNKNOWN
##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data,
##INFO=<ID=p-value1,Number=1,Type=Float,Description="A P-value">
##INFO=<ID=p-value2,Number=1,Type=Float,Description="A P-value">
##INFO=<ID=#Cm_Group[Group_1],Number=1,Type=Float,Description="Some count">
##FORMAT=<ID=Zygosity,Number=1,Type=String,Description="Zygosity">
##FORMAT=<ID=Another,Number=1,Type=String,Description="Another">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SampleA	SampleB

Creating base test directory: test-results/stats-writer
allele: A ref: [CC] alt: [T]23:20:11.292 INFO  TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0
23:20:11.292 INFO  TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds
[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 58.806 s - in TestSuite
23:20:11.625 INFO  GobyRengine - Shutdown hook is terminating R
[INFO] 
[INFO] Results:
[INFO] 
[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46
[INFO] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Goby Framework 3.3.1:
[INFO] 
[INFO] Goby Framework ..................................... SUCCESS [  0.038 s]
[INFO] Goby I/O ........................................... SUCCESS [  6.614 s]
[INFO] Goby Full Distribution ............................. SUCCESS [01:04 min]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:11 min
[INFO] Finished at: 2024-05-14T23:20:12Z
[INFO] ------------------------------------------------------------------------
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode -Ddebian.dir=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian -Ddebian.package=libgoby-io-java -Dmaven.repo.local=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
[WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16
[WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
[WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Goby Framework                                                     [pom]
[INFO] Goby I/O                                                           [jar]
[INFO] Goby Full Distribution                                             [jar]
[INFO] 
[INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
[INFO] Building Goby Framework 3.3.1                                      [1/3]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ goby-framework ---
[INFO] Cleaning pom file: /<<PKGBUILDDIR>>/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libgoby-io-java --has-package-version
[INFO] 	--rules=/<<PKGBUILDDIR>>/debian/maven.rules
[INFO] 	--ignore-rules=/<<PKGBUILDDIR>>/debian/maven.ignoreRules
[INFO] 	--published-rules=/<<PKGBUILDDIR>>/debian/maven.publishedRules
[INFO] 
[INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
[INFO] Building Goby I/O 3.3.1                                            [2/3]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ goby-io ---
[INFO] Cleaning pom file: /<<PKGBUILDDIR>>/goby-io/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libgoby-io-java
[INFO] 	--rules=/<<PKGBUILDDIR>>/debian/maven.rules
[INFO] 	--ignore-rules=/<<PKGBUILDDIR>>/debian/maven.ignoreRules
[INFO] 	--published-rules=/<<PKGBUILDDIR>>/debian/maven.publishedRules
[INFO] Install jar for goby-io into /usr/share/java
[INFO] 
[INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
[INFO] Building Goby Full Distribution 3.3.1                              [3/3]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ goby-distribution ---
[INFO] Cleaning pom file: /<<PKGBUILDDIR>>/goby-distribution/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=goby-java
[INFO] 	--rules=/<<PKGBUILDDIR>>/debian/maven.rules
[INFO] 	--ignore-rules=/<<PKGBUILDDIR>>/debian/maven.ignoreRules
[INFO] 	--published-rules=/<<PKGBUILDDIR>>/debian/maven.publishedRules
[INFO] Install jar for goby-distribution into /usr/share/java
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Goby Framework 3.3.1:
[INFO] 
[INFO] Goby Framework ..................................... SUCCESS [  0.230 s]
[INFO] Goby I/O ........................................... SUCCESS [  0.045 s]
[INFO] Goby Full Distribution ............................. SUCCESS [  0.033 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  0.414 s
[INFO] Finished at: 2024-05-14T23:20:13Z
[INFO] ------------------------------------------------------------------------
	mh_resolve_dependencies --non-interactive --offline --build -plibgoby-io-java --base-directory=/<<BUILDDIR>>/libgoby-java-3.3.1\+dfsg2 --non-explore
Analysing pom.xml...
Analysing goby-distribution/pom.xml...
Checking the parent dependency in the sub project goby-distribution/pom.xml
Analysing goby-io/pom.xml...
Checking the parent dependency in the sub project goby-io/pom.xml
> dpkg --search /usr/share/maven-repo/org/rosuda/REngine/REngine/*/* 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/maven-repo/org/rosuda/REngine/REngine
May 14, 2024 11:20:19 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve
SEVERE: Cannot resolve dependencies in /<<PKGBUILDDIR>>/goby-distribution/pom.xml: Dependency not found org.rosuda.REngine:REngine:jar:debian
> dpkg --search /usr/share/maven-repo/org/itadaki/bzip2/*/* 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/maven-repo/org/itadaki/bzip2
May 14, 2024 11:20:24 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve
SEVERE: Cannot resolve dependencies in /<<PKGBUILDDIR>>/goby-io/pom.xml: Dependency not found org.itadaki:bzip2:jar:debian
ERROR:
goby-distribution/pom.xml: dependency is not packaged in the Maven repository for Debian: org.rosuda.REngine:REngine:debian
goby-io/pom.xml: dependency is not packaged in the Maven repository for Debian: org.itadaki:bzip2:debian
--------
Some problems were found in this project, exiting...
	mh_unpatchpoms -plibgoby-io-java
   dh_install
   jh_installjavadoc
   dh_installdocs
   dh_installchangelogs
   dh_installman
   dh_lintian
   dh_perl
   dh_link
   jh_installlibs
   jh_classpath
   jh_manifest
   jh_exec
   jh_depends
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_installdeb
   dh_gencontrol
dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${maven:Depends} used, but is not defined
dpkg-gencontrol: warning: Recommends field of package goby-java: substitution variable ${maven:OptionalDepends} used, but is not defined
dpkg-gencontrol: warning: package goby-java: substitution variable ${java:Depends} unused, but is defined
dpkg-gencontrol: warning: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${java:Depends} unused, but is defined
dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${maven:CompileDepends} unused, but is defined
   dh_md5sums
   dh_builddeb
INFO: pkgstriptranslations version 154
INFO: pkgstriptranslations version 154
pkgstriptranslations: processing goby-java (in debian/goby-java); do_strip: , oemstrip: 
pkgstriptranslations: processing libgoby-io-java (in debian/libgoby-io-java); do_strip: , oemstrip: 
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgstripfiles: processing control file: debian/goby-java/DEBIAN/control, package goby-java, directory debian/goby-java
INFO: pkgstripfiles: waiting for lock (goby-java) ...
pkgstripfiles: processing control file: debian/libgoby-io-java/DEBIAN/control, package libgoby-io-java, directory debian/libgoby-io-java
pkgstripfiles: Truncating usr/share/doc/libgoby-io-java/changelog.Debian.gz to topmost ten records
pkgstripfiles: Running PNG optimization (using 4 cpus) for package libgoby-io-java ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-11_all.deb'.
Searching for duplicated docs in dependency libgoby-io-java...
  symlinking changelog.Debian.gz in goby-java to file in libgoby-io-java
pkgstripfiles: Running PNG optimization (using 4 cpus) for package goby-java ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'goby-java' in '../goby-java_3.3.1+dfsg2-11_all.deb'.
 dpkg-genbuildinfo --build=binary -O../libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo
 dpkg-genchanges --build=binary -mLaunchpad Build Daemon <buildd@lcy02-amd64-047.buildd> -O../libgoby-java_3.3.1+dfsg2-11_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2024-05-14T23:20:31Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


libgoby-java_3.3.1+dfsg2-11_amd64.changes:
------------------------------------------

Format: 1.8
Date: Tue, 14 May 2024 18:17:12 +0200
Source: libgoby-java
Binary: goby-java libgoby-io-java
Built-For-Profiles: noudeb
Architecture: all
Version: 3.3.1+dfsg2-11
Distribution: oracular-proposed
Urgency: medium
Maintainer: Launchpad Build Daemon <buildd@lcy02-amd64-047.buildd>
Changed-By: Pierre Gruet <pgt@debian.org>
Description:
 goby-java  - next-generation sequencing data and results analysis tool
 libgoby-io-java - IO API for goby
Changes:
 libgoby-java (3.3.1+dfsg2-11) unstable; urgency=medium
 .
   * Raising Standards version to 4.7.0 (no change)
   * Restricting autopkgtest architecture to amd64 and arm64, where sra-sdk
     packages are installable
   * Build-depending on pkgconf instead of obsolete pkg-config
Checksums-Sha1:
 fb82b6001d7beeb6a5292bfa1b612b3b975424c8 1535160 goby-java_3.3.1+dfsg2-11_all.deb
 298cebb5dcb6b8edf36d45ac0725b0df102d9f72 944424 libgoby-io-java_3.3.1+dfsg2-11_all.deb
 5d6c1cb6f9a51f0e1817281316a063e24c0c76cb 21822 libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo
Checksums-Sha256:
 986b41569f9be8bf75438f0eb162969660519d64d94d871a11435223b25a4c1b 1535160 goby-java_3.3.1+dfsg2-11_all.deb
 fa1cd5875380684486482cf01adf9a8d6f69079273b769f5c2a5fa7303bc0bc7 944424 libgoby-io-java_3.3.1+dfsg2-11_all.deb
 c43589df1244819000665d237944b769e3e169a2d2fe3fc81682461042da0e7f 21822 libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo
Files:
 354ac2306ab1fc35c20bfb4edac46a89 1535160 science optional goby-java_3.3.1+dfsg2-11_all.deb
 27942a8c567211b944f72f06fa3331a4 944424 science optional libgoby-io-java_3.3.1+dfsg2-11_all.deb
 99123a70d158f9ac2d58e1aa3bfa2270 21822 science optional libgoby-java_3.3.1+dfsg2-11_amd64.buildinfo
/<<BUILDDIR>>/libgoby-java_3.3.1+dfsg2-11_amd64.changes.new could not be renamed to /<<BUILDDIR>>/libgoby-java_3.3.1+dfsg2-11_amd64.changes: Illegal seek
Distribution field may be wrong!!!
+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: libgoby-java
Binary: goby-java libgoby-io-java
Architecture: all
Version: 3.3.1+dfsg2-11
Checksums-Md5:
 354ac2306ab1fc35c20bfb4edac46a89 1535160 goby-java_3.3.1+dfsg2-11_all.deb
 27942a8c567211b944f72f06fa3331a4 944424 libgoby-io-java_3.3.1+dfsg2-11_all.deb
Checksums-Sha1:
 fb82b6001d7beeb6a5292bfa1b612b3b975424c8 1535160 goby-java_3.3.1+dfsg2-11_all.deb
 298cebb5dcb6b8edf36d45ac0725b0df102d9f72 944424 libgoby-io-java_3.3.1+dfsg2-11_all.deb
Checksums-Sha256:
 986b41569f9be8bf75438f0eb162969660519d64d94d871a11435223b25a4c1b 1535160 goby-java_3.3.1+dfsg2-11_all.deb
 fa1cd5875380684486482cf01adf9a8d6f69079273b769f5c2a5fa7303bc0bc7 944424 libgoby-io-java_3.3.1+dfsg2-11_all.deb
Build-Origin: Ubuntu
Build-Architecture: amd64
Build-Date: Tue, 14 May 2024 23:20:30 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
 merged-usr-via-aliased-dirs
 usr-local-has-programs
Installed-Build-Depends:
 adduser (= 3.137ubuntu1),
 adwaita-icon-theme (= 46.0-1),
 ant (= 1.10.14-1),
 ant-contrib (= 1.0~b3+svn177-12),
 at-spi2-common (= 2.52.0-1build1),
 autoconf (= 2.71-3),
 automake (= 1:1.16.5-1.3ubuntu1),
 autopoint (= 0.21-14ubuntu2),
 autotools-dev (= 20220109.1),
 base-files (= 13.1ubuntu1),
 base-passwd (= 3.6.3build1),
 bash (= 5.2.21-2ubuntu4),
 binfmt-support (= 2.2.2-7),
 binutils (= 2.42-4ubuntu2),
 binutils-common (= 2.42-4ubuntu2),
 binutils-x86-64-linux-gnu (= 2.42-4ubuntu2),
 bsdextrautils (= 2.39.3-9ubuntu6),
 bsdutils (= 1:2.39.3-9ubuntu6),
 build-essential (= 12.10ubuntu1),
 bzip2 (= 1.0.8-5.1),
 ca-certificates (= 20240203),
 ca-certificates-java (= 20240118),
 coreutils (= 9.4-3ubuntu6),
 cpp (= 4:13.2.0-7ubuntu1),
 cpp-13 (= 13.2.0-25ubuntu1),
 cpp-13-x86-64-linux-gnu (= 13.2.0-25ubuntu1),
 cpp-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1),
 dash (= 0.5.12-6ubuntu5),
 dbus (= 1.14.10-4ubuntu4),
 dbus-bin (= 1.14.10-4ubuntu4),
 dbus-daemon (= 1.14.10-4ubuntu4),
 dbus-session-bus-common (= 1.14.10-4ubuntu4),
 dbus-system-bus-common (= 1.14.10-4ubuntu4),
 dbus-user-session (= 1.14.10-4ubuntu4),
 dconf-gsettings-backend (= 0.40.0-4build2),
 dconf-service (= 0.40.0-4build2),
 dctrl-tools (= 2.24-3build3),
 debconf (= 1.5.86ubuntu1),
 debhelper (= 13.14.1ubuntu5),
 debianutils (= 5.17build1),
 debugedit (= 1:5.0-5build2),
 default-jdk (= 2:1.21-75+exp1),
 default-jdk-headless (= 2:1.21-75+exp1),
 default-jre (= 2:1.21-75+exp1),
 default-jre-headless (= 2:1.21-75+exp1),
 devscripts (= 2.23.7ubuntu1),
 dh-autoreconf (= 20),
 dh-strip-nondeterminism (= 1.13.1-1),
 diffutils (= 1:3.10-1build1),
 dirmngr (= 2.4.4-2ubuntu17),
 dpkg (= 1.22.6ubuntu10),
 dpkg-dev (= 1.22.6ubuntu10),
 dwz (= 0.15-1build6),
 fastjar (= 2:0.98-7),
 file (= 1:5.45-3build1),
 findutils (= 4.9.0-5build1),
 fontconfig (= 2.15.0-1.1ubuntu2),
 fontconfig-config (= 2.15.0-1.1ubuntu2),
 fonts-dejavu-core (= 2.37-8),
 fonts-dejavu-mono (= 2.37-8),
 g++ (= 4:13.2.0-7ubuntu1),
 g++-13 (= 13.2.0-25ubuntu1),
 g++-13-x86-64-linux-gnu (= 13.2.0-25ubuntu1),
 g++-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1),
 gcc (= 4:13.2.0-7ubuntu1),
 gcc-13 (= 13.2.0-25ubuntu1),
 gcc-13-base (= 13.2.0-25ubuntu1),
 gcc-13-x86-64-linux-gnu (= 13.2.0-25ubuntu1),
 gcc-14-base (= 14-20240429-1ubuntu1),
 gcc-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1),
 gettext (= 0.21-14ubuntu2),
 gettext-base (= 0.21-14ubuntu2),
 gnupg (= 2.4.4-2ubuntu17),
 gnupg-utils (= 2.4.4-2ubuntu17),
 gpg (= 2.4.4-2ubuntu17),
 gpg-agent (= 2.4.4-2ubuntu17),
 gpgconf (= 2.4.4-2ubuntu17),
 gpgsm (= 2.4.4-2ubuntu17),
 gpgv (= 2.4.4-2ubuntu17),
 grep (= 3.11-4build1),
 groff-base (= 1.23.0-4),
 gtk-update-icon-cache (= 3.24.41-4ubuntu1),
 gzip (= 1.12-1ubuntu3),
 hicolor-icon-theme (= 0.17-2),
 hostname (= 3.23+nmu2ubuntu2),
 humanity-icon-theme (= 0.6.16),
 init-system-helpers (= 1.66ubuntu1),
 intltool-debian (= 0.35.0+20060710.6),
 jarwrapper (= 0.79),
 java-common (= 0.75+exp1),
 java-wrappers (= 0.4),
 javahelper (= 0.79),
 junit4 (= 4.13.2-4),
 junit5 (= 5.10.1-1),
 keyboxd (= 2.4.4-2ubuntu17),
 libacl1 (= 2.3.2-2),
 libactivation-java (= 1.2.0-2),
 libaopalliance-java (= 20070526-7),
 libapache-pom-java (= 29-2),
 libapiguardian-java (= 1.1.2-1),
 libapparmor1 (= 4.0.1-0ubuntu1),
 libarchive-zip-perl (= 1.68-1),
 libargon2-1 (= 0~20190702+dfsg-4build1),
 libasan8 (= 14-20240429-1ubuntu1),
 libasm-java (= 9.7-1),
 libasound2-data (= 1.2.11-1build2),
 libasound2t64 (= 1.2.11-1build2),
 libassuan0 (= 2.5.6-1build1),
 libatinject-jsr330-api-java (= 1.0+ds1-5),
 libatk-bridge2.0-0t64 (= 2.52.0-1build1),
 libatk1.0-0t64 (= 2.52.0-1build1),
 libatomic1 (= 14-20240429-1ubuntu1),
 libatspi2.0-0t64 (= 2.52.0-1build1),
 libattr1 (= 1:2.5.2-1build1),
 libaudit-common (= 1:3.1.2-2.1build1),
 libaudit1 (= 1:3.1.2-2.1build1),
 libavahi-client3 (= 0.8-13ubuntu6),
 libavahi-common-data (= 0.8-13ubuntu6),
 libavahi-common3 (= 0.8-13ubuntu6),
 libb-hooks-op-check-perl (= 0.22-3build1),
 libbarclay-java (= 5.0.0+dfsg-1),
 libbatik-java (= 1.17+dfsg-1),
 libbinutils (= 2.42-4ubuntu2),
 libblas3 (= 3.12.0-3build1),
 libblkid1 (= 2.39.3-9ubuntu6),
 libbrotli1 (= 1.1.0-2build2),
 libbsd0 (= 0.12.2-1),
 libbsh-java (= 2.0b4-20),
 libbuild-helper-maven-plugin-java (= 3.3.0-1),
 libbyte-buddy-java (= 1.14.13-1),
 libbz2-1.0 (= 1.0.8-5.1),
 libc-bin (= 2.39-0ubuntu8.1),
 libc-dev-bin (= 2.39-0ubuntu8.1),
 libc6 (= 2.39-0ubuntu8.1),
 libc6-dev (= 2.39-0ubuntu8.1),
 libcairo-gobject2 (= 1.18.0-3build1),
 libcairo2 (= 1.18.0-3build1),
 libcap-ng0 (= 0.8.5-1),
 libcap2 (= 1:2.66-5ubuntu2),
 libcc1-0 (= 14-20240429-1ubuntu1),
 libcdi-api-java (= 1.2-3),
 libclass-method-modifiers-perl (= 2.15-1),
 libclass-xsaccessor-perl (= 1.19-4build4),
 libclone-perl (= 0.46-1build3),
 libcolord2 (= 1.4.7-1build2),
 libcolt-free-java (= 1.2.0+dfsg-8),
 libcom-err2 (= 1.47.0-2.4~exp1ubuntu4),
 libcommons-beanutils-java (= 1.9.4-2),
 libcommons-cli-java (= 1.6.0-1),
 libcommons-codec-java (= 1.16.0-1),
 libcommons-collections3-java (= 3.2.2-3),
 libcommons-collections4-java (= 4.4-2),
 libcommons-compress-java (= 1.25.0-1),
 libcommons-configuration-java (= 1.10-6),
 libcommons-digester-java (= 1.8.1-6),
 libcommons-exec-java (= 1.3-2),
 libcommons-io-java (= 2.16.1-1),
 libcommons-jexl2-java (= 2.1.1-6),
 libcommons-lang-java (= 2.6-10),
 libcommons-lang3-java (= 3.14.0-1),
 libcommons-logging-java (= 1.3.0-1ubuntu1),
 libcommons-math-java (= 2.2-8),
 libcommons-math3-java (= 3.6.1-3),
 libcommons-parent-java (= 56-1),
 libcommons-text-java (= 1.11.0-1),
 libcommons-validator-java (= 1:1.7-1),
 libcrypt-dev (= 1:4.4.36-4build1),
 libcrypt1 (= 1:4.4.36-4build1),
 libcryptsetup12 (= 2:2.7.0-1ubuntu4),
 libctf-nobfd0 (= 2.42-4ubuntu2),
 libctf0 (= 2.42-4ubuntu2),
 libcups2t64 (= 2.4.7-1.2ubuntu7),
 libcurl4t64 (= 8.5.0-2ubuntu10.1),
 libdatrie1 (= 0.2.13-3build1),
 libdb5.3t64 (= 5.3.28+dfsg2-7),
 libdbus-1-3 (= 1.14.10-4ubuntu4),
 libdconf1 (= 0.40.0-4build2),
 libdebconfclient0 (= 0.271ubuntu3),
 libdebhelper-perl (= 13.14.1ubuntu5),
 libdeflate0 (= 1.20-1),
 libdevel-callchecker-perl (= 0.009-1),
 libdevmapper1.02.1 (= 2:1.02.185-3ubuntu3),
 libdistlib-java (= 1.0-4),
 libdom4j-java (= 2.1.4-1),
 libdoxia-core-java (= 1.12.0-1),
 libdoxia-java (= 1.12.0-1),
 libdoxia-sitetools-java (= 1.11.1-1),
 libdpkg-perl (= 1.22.6ubuntu10),
 libdrm-amdgpu1 (= 2.4.120-2build1),
 libdrm-common (= 2.4.120-2build1),
 libdrm-intel1 (= 2.4.120-2build1),
 libdrm-nouveau2 (= 2.4.120-2build1),
 libdrm-radeon1 (= 2.4.120-2build1),
 libdrm2 (= 2.4.120-2build1),
 libdsiutils-java (= 2.7.3+dfsg-1),
 libdw1t64 (= 0.191-1),
 libdynaloader-functions-perl (= 0.003-3),
 libeasymock-java (= 5.2.0-1),
 libedit2 (= 3.1-20230828-1build1),
 libel-api-java (= 3.0.0-3),
 libelf1t64 (= 0.191-1),
 libencode-locale-perl (= 1.05-3),
 libepoxy0 (= 1.5.10-1build1),
 liberror-prone-java (= 2.18.0-1),
 libexec-maven-plugin-java (= 3.1.0-2),
 libexpat1 (= 2.6.2-1),
 libfastutil-java (= 8.5.12+dfsg-2),
 libfdisk1 (= 2.39.3-9ubuntu6),
 libffi8 (= 3.4.6-1build1),
 libfile-dirlist-perl (= 0.05-3),
 libfile-homedir-perl (= 1.006-2),
 libfile-listing-perl (= 6.16-1),
 libfile-stripnondeterminism-perl (= 1.13.1-1),
 libfile-touch-perl (= 0.12-2),
 libfile-which-perl (= 1.27-2),
 libfontbox2-java (= 2.0.29-1),
 libfontconfig1 (= 2.15.0-1.1ubuntu2),
 libfop-java (= 1:2.8-3),
 libfreemarker-java (= 2.3.32-2),
 libfreetype6 (= 2.13.2+dfsg-1build3),
 libfribidi0 (= 1.0.13-3build1),
 libgatk-native-bindings-java (= 1.0.0+dfsg-2),
 libgcc-13-dev (= 13.2.0-25ubuntu1),
 libgcc-s1 (= 14-20240429-1ubuntu1),
 libgcrypt20 (= 1.10.3-2build1),
 libgdbm-compat4t64 (= 1.23-5.1build1),
 libgdbm6t64 (= 1.23-5.1build1),
 libgdk-pixbuf-2.0-0 (= 2.42.10+dfsg-3ubuntu3),
 libgdk-pixbuf2.0-common (= 2.42.10+dfsg-3ubuntu3),
 libgeronimo-annotation-1.3-spec-java (= 1.3-1),
 libgeronimo-interceptor-3.0-spec-java (= 1.0.1-4fakesync),
 libgfortran5 (= 14-20240429-1ubuntu1),
 libgif7 (= 5.2.2-1ubuntu1),
 libgkl-java (= 0.8.11+dfsg-2build1),
 libgl1 (= 1.7.0-1build1),
 libgl1-mesa-dri (= 24.0.7-1ubuntu1),
 libglapi-mesa (= 24.0.7-1ubuntu1),
 libglib2.0-0t64 (= 2.80.1-0ubuntu2),
 libglvnd0 (= 1.7.0-1build1),
 libglx-mesa0 (= 24.0.7-1ubuntu1),
 libglx0 (= 1.7.0-1build1),
 libgmp10 (= 2:6.3.0+dfsg-2ubuntu6),
 libgnutls30t64 (= 3.8.5-2ubuntu1),
 libgomp1 (= 14-20240429-1ubuntu1),
 libgoogle-gson-java (= 2.10.1-1),
 libgpg-error0 (= 1.49-2),
 libgprofng0 (= 2.42-4ubuntu2),
 libgraphite2-3 (= 1.3.14-2build1),
 libgssapi-krb5-2 (= 1.20.1-6ubuntu2),
 libgtk-3-0t64 (= 3.24.41-4ubuntu1),
 libgtk-3-common (= 3.24.41-4ubuntu1),
 libguava-java (= 32.0.1-1),
 libguice-java (= 4.2.3-2),
 libhamcrest-java (= 2.2-2),
 libharfbuzz0b (= 8.3.0-2build2),
 libhogweed6t64 (= 3.9.1-2.2build1),
 libhtml-parser-perl (= 3.82-1),
 libhtml-tagset-perl (= 3.24-1),
 libhtml-tree-perl (= 5.07-3),
 libhtsjdk-java (= 4.1.0+dfsg-1),
 libhttp-cookies-perl (= 6.11-1),
 libhttp-date-perl (= 6.06-1),
 libhttp-message-perl (= 6.45-1ubuntu1),
 libhttp-negotiate-perl (= 6.01-2),
 libhttpclient-java (= 4.5.14-1),
 libhttpcore-java (= 4.4.16-1),
 libhwasan0 (= 14-20240429-1ubuntu1),
 libicb-utils-java (= 2.0.1+git20161002.afee1d9-5),
 libice6 (= 2:1.0.10-1build3),
 libicu4j-java (= 73.2-1),
 libicu74 (= 74.2-1ubuntu3),
 libidn2-0 (= 2.3.7-2build1),
 libimport-into-perl (= 1.002005-2),
 libio-html-perl (= 1.004-3),
 libio-pty-perl (= 1:1.20-1build2),
 libio-socket-ssl-perl (= 2.085-1),
 libipc-run-perl (= 20231003.0-2),
 libisl23 (= 0.26-3build1),
 libitext1-java (= 1.4-7),
 libitm1 (= 14-20240429-1ubuntu1),
 libjansi-java (= 2.4.1-2),
 libjansson4 (= 2.14-2build2),
 libjavassist-java (= 1:3.27.0-1),
 libjaxb-api-java (= 2.3.1-1),
 libjaxen-java (= 1.1.6-4),
 libjaxp1.3-java (= 1.3.05-6),
 libjbig0 (= 2.1-6.1ubuntu2),
 libjboss-logging-java (= 3.5.3-1),
 libjboss-vfs-java (= 3.2.15.Final-3),
 libjbzip2-java (= 0.9.1-8),
 libjcommander-java (= 1.71-4),
 libjetty9-java (= 9.4.54-1),
 libjoptsimple-java (= 5.0.4-4),
 libjpeg-turbo8 (= 2.1.5-2ubuntu2),
 libjpeg8 (= 8c-2ubuntu11),
 libjsap-java (= 2.1-5),
 libjson-c5 (= 0.17-1build1),
 libjsoup-java (= 1.15.3-1),
 libjsp-api-java (= 2.3.4-3),
 libjsr305-java (= 0.1~+svn49-11),
 libjtidy-java (= 7+svn20110807-5),
 libk5crypto3 (= 1.20.1-6ubuntu2),
 libkeyutils1 (= 1.6.3-3build1),
 libkrb5-3 (= 1.20.1-6ubuntu2),
 libkrb5support0 (= 1.20.1-6ubuntu2),
 libksba8 (= 1.6.6-1build1),
 liblapack3 (= 3.12.0-3build1),
 liblcms2-2 (= 2.14-2build1),
 libldap2 (= 2.6.7+dfsg-1~exp1ubuntu8),
 liblerc4 (= 4.0.0+ds-4ubuntu2),
 liblightcouch-java (= 0.2.0-1),
 libllvm17t64 (= 1:17.0.6-12),
 liblog4j1.2-java (= 1.2.17-11),
 liblog4j2-java (= 2.19.0-2),
 liblogback-java (= 1:1.2.11-5),
 liblsan0 (= 14-20240429-1ubuntu1),
 liblwp-mediatypes-perl (= 6.04-2),
 liblwp-protocol-https-perl (= 6.14-1),
 liblzma5 (= 5.6.1+really5.4.5-1),
 libmagic-mgc (= 1:5.45-3build1),
 libmagic1t64 (= 1:5.45-3build1),
 libmaven-antrun-plugin-java (= 3.1.0-1),
 libmaven-archiver-java (= 3.6.0-1),
 libmaven-artifact-transfer-java (= 0.13.1-2),
 libmaven-assembly-plugin-java (= 3.4.2-1),
 libmaven-clean-plugin-java (= 3.2.0-2),
 libmaven-common-artifact-filters-java (= 3.3.2-1),
 libmaven-compiler-plugin-java (= 3.10.1-2),
 libmaven-dependency-analyzer-java (= 1.13.0-1),
 libmaven-dependency-plugin-java (= 3.5.0-1),
 libmaven-dependency-tree-java (= 3.2.1-1),
 libmaven-file-management-java (= 3.0.0-1),
 libmaven-filtering-java (= 3.3.0-1),
 libmaven-invoker-java (= 3.2.0-1),
 libmaven-jar-plugin-java (= 3.3.0-2),
 libmaven-javadoc-plugin-java (= 3.4.1-3),
 libmaven-parent-java (= 35-1),
 libmaven-plugin-tools-java (= 3.7.1-1),
 libmaven-reporting-api-java (= 3.1.1-1),
 libmaven-reporting-exec-java (= 1.6.0-1),
 libmaven-reporting-impl-java (= 3.2.0-2),
 libmaven-resolver-java (= 1.6.3-1),
 libmaven-resources-plugin-java (= 3.3.0-1),
 libmaven-shared-incremental-java (= 1.1-4),
 libmaven-shared-io-java (= 3.0.0-4),
 libmaven-shared-utils-java (= 3.3.4-1),
 libmaven-site-plugin-java (= 3.12.1-2),
 libmaven-source-plugin-java (= 3.2.1-2),
 libmaven3-core-java (= 3.8.7-2),
 libmbedcrypto7t64 (= 2.28.8-1),
 libmbedtls14t64 (= 2.28.8-1),
 libmbedx509-1t64 (= 2.28.8-1),
 libmd0 (= 1.1.0-2build1),
 libmjson-java (= 1.4.0-3),
 libmodule-runtime-perl (= 0.016-2),
 libmongodb-java (= 3.6.3-2),
 libmoo-perl (= 2.005005-1),
 libmount1 (= 2.39.3-9ubuntu6),
 libmpc3 (= 1.3.1-1build1),
 libmpfr6 (= 4.2.1-1build1),
 libncbi-ngs3 (= 3.0.3+dfsg-6ubuntu5),
 libncbi-vdb3 (= 3.0.2+dfsg-2build2),
 libncursesw6 (= 6.4+20240113-1ubuntu2),
 libnet-http-perl (= 6.23-1),
 libnet-ssleay-perl (= 1.94-1build4),
 libnettle8t64 (= 3.9.1-2.2build1),
 libnghttp2-14 (= 1.61.0-1),
 libngs-java (= 3.0.3+dfsg-6ubuntu5),
 libngs-jni (= 3.0.3+dfsg-6ubuntu5),
 libnpth0t64 (= 1.6-3.1build1),
 libnspr4 (= 2:4.35-1.1build1),
 libnss3 (= 2:3.99-1),
 libobjenesis-java (= 3.3-3),
 libopentest4j-java (= 1.2.0-4),
 libopentest4j-reporting-java (= 0.1.0-M1-2),
 liboro-java (= 2.0.8a-14),
 libp11-kit0 (= 0.25.3-4ubuntu2),
 libpam-modules (= 1.5.3-7ubuntu1),
 libpam-modules-bin (= 1.5.3-7ubuntu1),
 libpam-runtime (= 1.5.3-7ubuntu1),
 libpam-systemd (= 256~rc1-1~exp2ubuntu1),
 libpam0g (= 1.5.3-7ubuntu1),
 libpango-1.0-0 (= 1.52.2+ds-1),
 libpangocairo-1.0-0 (= 1.52.2+ds-1),
 libpangoft2-1.0-0 (= 1.52.2+ds-1),
 libpaper-utils (= 1.1.29build1),
 libpaper1 (= 1.1.29build1),
 libparams-classify-perl (= 0.015-2build5),
 libpciaccess0 (= 0.17-3build1),
 libpcre2-8-0 (= 10.42-4ubuntu2),
 libpcsclite1 (= 2.2.1-1),
 libperl5.38t64 (= 5.38.2-4),
 libpicard-java (= 3.1.1+dfsg-1),
 libpicocli-java (= 4.6.2-2),
 libpipeline1 (= 1.5.7-2),
 libpixman-1-0 (= 0.42.2-1build1),
 libpj-java (= 0.0~20150107+dfsg-5),
 libpkgconf3 (= 1.8.1-2build1),
 libplexus-ant-factory-java (= 1.0~alpha2.1-4),
 libplexus-archiver-java (= 4.6.1-1),
 libplexus-bsh-factory-java (= 1.0~alpha7-5),
 libplexus-build-api-java (= 0.0.7-4),
 libplexus-cipher-java (= 2.0-1),
 libplexus-classworlds-java (= 2.7.0-1),
 libplexus-compiler-java (= 2.12.1-2),
 libplexus-component-annotations-java (= 2.1.1-1),
 libplexus-container-default-java (= 2.1.1-1),
 libplexus-container-default1.5-java (= 2.1.1-1),
 libplexus-i18n-java (= 1.0-beta-10-6),
 libplexus-interactivity-api-java (= 1.1-2),
 libplexus-interpolation-java (= 1.26-1),
 libplexus-io-java (= 3.3.1-2),
 libplexus-languages-java (= 1.1.1-2),
 libplexus-sec-dispatcher-java (= 2.0-3),
 libplexus-utils2-java (= 3.4.2-1),
 libplexus-velocity-java (= 1.2-3.1),
 libpng16-16t64 (= 1.6.43-5build1),
 libproc2-0 (= 2:4.0.4-4ubuntu3),
 libprotobuf-dev (= 3.21.12-8.2build1),
 libprotobuf-java (= 3.21.12-8.2build1),
 libprotobuf-lite32t64 (= 3.21.12-8.2build1),
 libprotobuf32t64 (= 3.21.12-8.2build1),
 libprotoc32t64 (= 3.21.12-8.2build1),
 libpsl5t64 (= 0.21.2-1.1build1),
 libpython3-stdlib (= 3.12.3-0ubuntu1),
 libpython3.12-minimal (= 3.12.3-1),
 libpython3.12-stdlib (= 3.12.3-1),
 libqdox-java (= 1.12.1-3),
 libqdox2-java (= 2.0.3-1),
 libquadmath0 (= 14-20240429-1ubuntu1),
 libreadline8t64 (= 8.2-4build1),
 libreflections-java (= 0.10.2+dfsg-2),
 librhino-java (= 1.7.14-2.1),
 librole-tiny-perl (= 2.002004-1),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2build7),
 libsasl2-2 (= 2.1.28+dfsg1-5ubuntu3),
 libsasl2-modules-db (= 2.1.28+dfsg1-5ubuntu3),
 libseccomp2 (= 2.5.5-1ubuntu3),
 libselinux1 (= 3.5-2ubuntu2),
 libsemanage-common (= 3.5-1build5),
 libsemanage2 (= 3.5-1build5),
 libsensors-config (= 1:3.6.0-9build1),
 libsensors5 (= 1:3.6.0-9build1),
 libsepol2 (= 3.5-2build1),
 libservlet-api-java (= 4.0.1-2),
 libsframe1 (= 2.42-4ubuntu2),
 libsharpyuv0 (= 1.4.0-0.1),
 libsisu-inject-java (= 0.3.4-2),
 libsisu-plexus-java (= 0.3.4-3),
 libslf4j-java (= 1.7.32-1),
 libsm6 (= 2:1.2.3-1build3),
 libsmartcols1 (= 2.39.3-9ubuntu6),
 libsnappy-java (= 1.1.10.5-2),
 libsnappy-jni (= 1.1.10.5-2),
 libsnappy1v5 (= 1.2.0-2),
 libsqlite3-0 (= 3.45.3-1),
 libssh-4 (= 0.10.6-2build2),
 libssl3t64 (= 3.0.13-0ubuntu3),
 libstdc++-13-dev (= 13.2.0-25ubuntu1),
 libstdc++6 (= 14-20240429-1ubuntu1),
 libsub-override-perl (= 0.10-1),
 libsub-quote-perl (= 2.006008-1ubuntu1),
 libsurefire-java (= 2.22.3-2),
 libsystemd-shared (= 256~rc1-1~exp2ubuntu1),
 libsystemd0 (= 256~rc1-1~exp2ubuntu1),
 libtasn1-6 (= 4.19.0-3build1),
 libtcl8.6 (= 8.6.14+dfsg-1build1),
 libthai-data (= 0.1.29-2build1),
 libthai0 (= 0.1.29-2build1),
 libtiff6 (= 4.5.1+git230720-4ubuntu2),
 libtimedate-perl (= 2.3300-2),
 libtinfo6 (= 6.4+20240113-1ubuntu2),
 libtirpc-common (= 1.3.4+ds-1.3),
 libtirpc3t64 (= 1.3.4+ds-1.3),
 libtk8.6 (= 8.6.14-1build1),
 libtool (= 2.4.7-7build1),
 libtry-tiny-perl (= 0.31-2),
 libtsan2 (= 14-20240429-1ubuntu1),
 libubsan1 (= 14-20240429-1ubuntu1),
 libuchardet0 (= 0.0.8-1build1),
 libudev1 (= 256~rc1-1~exp2ubuntu1),
 libunistring5 (= 1.2-1),
 libunivocity-parsers-java (= 2.9.1-1),
 liburi-perl (= 5.28-1),
 libuuid1 (= 2.39.3-9ubuntu6),
 libvelocity-tools-java (= 2.0-9),
 libvulkan1 (= 1.3.280.0-1),
 libwagon-file-java (= 3.5.3-1),
 libwagon-http-shaded-java (= 3.5.3-1),
 libwagon-provider-api-java (= 3.5.3-1),
 libwayland-client0 (= 1.22.0-2.1build1),
 libwayland-cursor0 (= 1.22.0-2.1build1),
 libwayland-egl1 (= 1.22.0-2.1build1),
 libwebp7 (= 1.4.0-0.1),
 libwebsocket-api-java (= 1.1-2),
 libwww-perl (= 6.77-1),
 libwww-robotrules-perl (= 6.02-1),
 libx11-6 (= 2:1.8.7-1build1),
 libx11-data (= 2:1.8.7-1build1),
 libx11-xcb1 (= 2:1.8.7-1build1),
 libxalan2-java (= 2.7.2-4),
 libxau6 (= 1:1.0.9-1build6),
 libxbean-reflect-java (= 4.5-8),
 libxcb-dri2-0 (= 1.15-1ubuntu2),
 libxcb-dri3-0 (= 1.15-1ubuntu2),
 libxcb-glx0 (= 1.15-1ubuntu2),
 libxcb-present0 (= 1.15-1ubuntu2),
 libxcb-randr0 (= 1.15-1ubuntu2),
 libxcb-render0 (= 1.15-1ubuntu2),
 libxcb-shm0 (= 1.15-1ubuntu2),
 libxcb-sync1 (= 1.15-1ubuntu2),
 libxcb-xfixes0 (= 1.15-1ubuntu2),
 libxcb1 (= 1.15-1ubuntu2),
 libxcomposite1 (= 1:0.4.5-1build3),
 libxcursor1 (= 1:1.2.1-1build1),
 libxdamage1 (= 1:1.1.6-1build1),
 libxdmcp6 (= 1:1.1.3-0ubuntu6),
 libxerces2-java (= 2.12.2-1),
 libxext6 (= 2:1.3.4-1build2),
 libxfixes3 (= 1:6.0.0-2build1),
 libxft2 (= 2.3.6-1build1),
 libxi6 (= 2:1.8.1-1build1),
 libxinerama1 (= 2:1.1.4-3build1),
 libxkbcommon0 (= 1.6.0-1build1),
 libxml-commons-external-java (= 1.4.01-6),
 libxml-commons-resolver1.1-java (= 1.2-11),
 libxml2 (= 2.9.14+dfsg-1.3ubuntu3),
 libxml2-utils (= 2.9.14+dfsg-1.3ubuntu3),
 libxmlgraphics-commons-java (= 2.8-2),
 libxpp3-java (= 1.1.4c-3),
 libxrandr2 (= 2:1.5.4-1),
 libxrender1 (= 1:0.9.10-1.1build1),
 libxshmfence1 (= 1.3-1build5),
 libxss1 (= 1:1.2.3-1build3),
 libxstream-java (= 1.4.20-1),
 libxt6t64 (= 1:1.2.1-1.2build1),
 libxtst6 (= 2:1.2.3-1.1build1),
 libxxf86vm1 (= 1:1.1.4-1build4),
 libxz-java (= 1.9-1),
 libzstd1 (= 1.5.5+dfsg2-2build1),
 linux-libc-dev (= 6.8.0-31.31),
 login (= 1:4.13+dfsg1-4ubuntu3),
 lto-disabled-list (= 48),
 m4 (= 1.4.19-4build1),
 make (= 4.3-4.1build2),
 man-db (= 2.12.1-1),
 maven (= 3.8.7-2),
 maven-debian-helper (= 2.6.4),
 maven-repo-helper (= 1.11),
 mawk (= 1.3.4.20240123-1build1),
 media-types (= 10.1.0),
 mount (= 2.39.3-9ubuntu6),
 ncbi-vdb-data (= 3.0.2+dfsg-2build2),
 ncurses-base (= 6.4+20240113-1ubuntu2),
 ncurses-bin (= 6.4+20240113-1ubuntu2),
 netbase (= 6.4),
 openjdk-21-jdk (= 21.0.3+9-1ubuntu1),
 openjdk-21-jdk-headless (= 21.0.3+9-1ubuntu1),
 openjdk-21-jre (= 21.0.3+9-1ubuntu1),
 openjdk-21-jre-headless (= 21.0.3+9-1ubuntu1),
 openssl (= 3.0.13-0ubuntu3),
 passwd (= 1:4.13+dfsg1-4ubuntu3),
 patch (= 2.7.6-7build3),
 patchutils (= 0.4.2-1build3),
 perl (= 5.38.2-4),
 perl-base (= 5.38.2-4),
 perl-modules-5.38 (= 5.38.2-4),
 perl-openssl-defaults (= 7build3),
 pinentry-curses (= 1.2.1-3ubuntu5),
 pkgconf (= 1.8.1-2build1),
 pkgconf-bin (= 1.8.1-2build1),
 po-debconf (= 1.0.21+nmu1),
 procps (= 2:4.0.4-4ubuntu3),
 protobuf-compiler (= 3.21.12-8.2build1),
 python3 (= 3.12.3-0ubuntu1),
 python3-minimal (= 3.12.3-0ubuntu1),
 python3.12 (= 3.12.3-1),
 python3.12-minimal (= 3.12.3-1),
 r-base-core (= 4.4.0-2),
 r-cran-rjava (= 1.0-11-1),
 readline-common (= 8.2-4build1),
 rpcsvc-proto (= 1.4.2-0ubuntu7),
 sed (= 4.9-2build1),
 sensible-utils (= 0.0.22),
 sgml-base (= 1.31),
 shared-mime-info (= 2.4-4),
 systemd (= 256~rc1-1~exp2ubuntu1),
 systemd-dev (= 256~rc1-1~exp2ubuntu1),
 systemd-sysv (= 256~rc1-1~exp2ubuntu1),
 sysvinit-utils (= 3.08-6ubuntu3),
 tar (= 1.35+dfsg-3build1),
 testng (= 6.9.12-4),
 tzdata (= 2024a-4ubuntu1),
 ubuntu-mono (= 24.04-0ubuntu1),
 ucf (= 3.0043+nmu1),
 unzip (= 6.0-28ubuntu4),
 util-linux (= 2.39.3-9ubuntu6),
 velocity (= 1.7-7),
 wdiff (= 1.2.2-6build1),
 x11-common (= 1:7.7+23ubuntu3),
 xdg-utils (= 1.1.3-4.1ubuntu3),
 xkb-data (= 2.41-2ubuntu1),
 xz-utils (= 5.6.1+really5.4.5-1),
 zip (= 3.0-13build1),
 zlib1g (= 1:1.3.dfsg-3.1ubuntu2),
 zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2)
Environment:
 DEB_BUILD_OPTIONS="parallel=4"
 DEB_BUILD_PROFILES="noudeb"
 LANG="C.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1715703432"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


goby-java_3.3.1+dfsg2-11_all.deb
--------------------------------

 new Debian package, version 2.0.
 size 1535160 bytes: control archive=971 bytes.
    1086 bytes,    23 lines      control
     513 bytes,     6 lines      md5sums
 Package: goby-java
 Source: libgoby-java
 Version: 3.3.1+dfsg2-11
 Architecture: all
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1668
 Depends: default-jre, libgoby-io-java (= 3.3.1+dfsg2-11), libdistlib-java, libjaxb-api-java, r-cran-rjava
 Section: science
 Priority: optional
 Homepage: https://campagnelab.org/software/goby/
 Description: next-generation sequencing data and results analysis tool
  Goby is a next-gen data management framework designed to facilitate the
  implementation of efficient data analysis pipelines.
  .
  Goby provides very efficient file formats to store next-generation sequencing
  data and intermediary analysis results.
  .
  Goby also provides utilities that implement common next-gen data computations.
  These utilities are designed to be relatively easy to use, yet very efficient.
  .
  This package provides the entire Goby framework, including application
  programs (i.e., Goby modes). It is released under the GPL3 license.

drwxr-xr-x root/root         0 2024-05-14 16:17 ./
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/bin/
-rwxr-xr-x root/root      1935 2024-05-14 16:17 ./usr/bin/goby
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/doc/goby-java/
lrwxrwxrwx root/root         0 2024-05-14 16:17 ./usr/share/doc/goby-java/changelog.Debian.gz -> ../libgoby-io-java/changelog.Debian.gz
-rw-r--r-- root/root     11109 2023-12-03 06:58 ./usr/share/doc/goby-java/copyright
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/java/
-rw-r--r-- root/root   1648083 2024-05-14 16:17 ./usr/share/java/goby-distribution-3.3.1.jar
lrwxrwxrwx root/root         0 2024-05-14 16:17 ./usr/share/java/goby-distribution.jar -> goby-distribution-3.3.1.jar
lrwxrwxrwx root/root         0 2024-05-14 16:17 ./usr/share/java/goby.jar -> goby-distribution.jar
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/man/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/man/man1/
-rw-r--r-- root/root      1445 2024-05-14 16:17 ./usr/share/man/man1/goby.1.gz
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-distribution/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-distribution/3.3.1/
lrwxrwxrwx root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-distribution/3.3.1/goby-distribution-3.3.1.jar -> ../../../../../../java/goby-distribution-3.3.1.jar
-rw-r--r-- root/root      9459 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-distribution/3.3.1/goby-distribution-3.3.1.pom
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-distribution/debian/
lrwxrwxrwx root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-distribution/debian/goby-distribution-debian.jar -> ../../../../../../java/goby-distribution-3.3.1.jar
-rw-r--r-- root/root      9460 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-distribution/debian/goby-distribution-debian.pom


libgoby-io-java_3.3.1+dfsg2-11_all.deb
--------------------------------------

 new Debian package, version 2.0.
 size 944424 bytes: control archive=1099 bytes.
    1288 bytes,    20 lines      control
     767 bytes,     8 lines      md5sums
 Package: libgoby-io-java
 Source: libgoby-java
 Version: 3.3.1+dfsg2-11
 Architecture: all
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1035
 Depends: libcommons-cli-java (>= 1.6.0), libcommons-configuration-java, libcommons-exec-java (>= 1.3), libcommons-io-java (>= 2.16.1), libcommons-lang-java (>= 2.6), libcommons-logging-java (>= 1.3.0), libcommons-math-java (>= 2.2), libdsiutils-java, libfastutil-java, libguava-java, libhtsjdk-java (>= 3.0.2), libicb-utils-java, libjsap-java (>= 2.1), libprotobuf-java, libreflections-java, libslf4j-java (>= 1.7.32), libxstream-java (>= 1.4.20), libcommons-collections3-java, libjbzip2-java, libpj-java
 Section: science
 Priority: optional
 Homepage: https://campagnelab.org/software/goby/
 Description: IO API for goby
  Goby is a next-gen data management framework designed to facilitate the
  implementation of efficient data analysis pipelines.
  .
  Goby provides very efficient file formats to store next-generation sequencing
  data and intermediary analysis results.
  .
  This package contains the Goby IO API, including code necessary to read and
  write Goby file formats. It is released under the LGPL3 license.

drwxr-xr-x root/root         0 2024-05-14 16:17 ./
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/doc/libgoby-io-java/
-rw-r--r-- root/root      1111 2024-05-14 16:17 ./usr/share/doc/libgoby-io-java/changelog.Debian.gz
-rw-r--r-- root/root     11109 2023-12-03 06:58 ./usr/share/doc/libgoby-io-java/copyright
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/java/
-rw-r--r-- root/root   1008251 2024-05-14 16:17 ./usr/share/java/goby-io-3.3.1.jar
lrwxrwxrwx root/root         0 2024-05-14 16:17 ./usr/share/java/goby-io.jar -> goby-io-3.3.1.jar
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/lintian/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/lintian/overrides/
-rw-r--r-- root/root       134 2021-08-09 11:35 ./usr/share/lintian/overrides/libgoby-io-java
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-framework/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-framework/3.3.1/
-rw-r--r-- root/root      1298 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-framework/3.3.1/goby-framework-3.3.1.pom
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-framework/debian/
-rw-r--r-- root/root      1299 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-framework/debian/goby-framework-debian.pom
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-io/
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-io/3.3.1/
lrwxrwxrwx root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-io/3.3.1/goby-io-3.3.1.jar -> ../../../../../../java/goby-io-3.3.1.jar
-rw-r--r-- root/root      4946 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-io/3.3.1/goby-io-3.3.1.pom
drwxr-xr-x root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-io/debian/
lrwxrwxrwx root/root         0 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-io/debian/goby-io-debian.jar -> ../../../../../../java/goby-io-3.3.1.jar
-rw-r--r-- root/root      4947 2024-05-14 16:17 ./usr/share/maven-repo/org/campagnelab/goby/goby-io/debian/goby-io-debian.pom


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not removing build depends: as requested

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Type: binary
Build-Space: 212696
Build-Time: 134
Distribution: oracular-proposed
Host Architecture: amd64
Install-Time: 48
Job: libgoby-java_3.3.1+dfsg2-11.dsc
Machine Architecture: amd64
Package: libgoby-java
Package-Time: 183
Source-Version: 3.3.1+dfsg2-11
Space: 212696
Status: successful
Version: 3.3.1+dfsg2-11
--------------------------------------------------------------------------------
Finished at 2024-05-14T23:20:31Z
Build needed 00:03:03, 212696k disk space
RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28446411
Scanning for processes to kill in build PACKAGEBUILD-28446411