https://launchpad.net/ubuntu/+source/htslib/1.19+ds-1.1build3/+build/27988872 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos03-arm64-021 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 aarch64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~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... 31 Mar 19:05:19 ntpdate[1876]: adjust time server 10.211.37.1 offset -0.001595 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27988872 --image-type chroot /home/buildd/filecache-default/59612f0fc5bae33f6226b6e60c2e882b82c04bd0 Creating target for build PACKAGEBUILD-27988872 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27988872 Starting target for build PACKAGEBUILD-27988872 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27988872 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27988872 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27988872 Updating target for build PACKAGEBUILD-27988872 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [89.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main armhf Packages [1336 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6118 kB] Get:9 http://ftpmaster.internal/ubuntu noble-updates/main armhf Packages [666 kB] Get:10 http://ftpmaster.internal/ubuntu noble-updates/main Translation-en [242 kB] Get:11 http://ftpmaster.internal/ubuntu noble-updates/universe armhf Packages [4423 kB] Get:12 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [1693 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [440 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [183 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [1283 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [556 kB] Fetched 32.3 MB in 5s (6282 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 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* libperl5.36* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-arm-linux-gnueabihf cpp-arm-linux-gnueabihf g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-13-arm-linux-gnueabihf gcc-14-base gcc-arm-linux-gnueabihf 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 have been kept back: libaudit1 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-arm-linux-gnueabihf binutils-common bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot 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 libatomic1 libattr1 libaudit-common 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 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0 libip4tc2 libjansson4 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 153 upgraded, 23 newly installed, 15 to remove and 1 not upgraded. Need to get 96.8 MB of archives. After this operation, 24.8 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnsl-dev armhf 1.3.0-3build3 [66.2 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main armhf libcrypt-dev armhf 1:4.4.36-4 [136 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6-dev armhf 2.39-0ubuntu8 [1352 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-dev-bin armhf 2.39-0ubuntu8 [19.1 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc-dev armhf 1.3.4+ds-1.1build1 [184 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf libnss-nisplus armhf 1.3-5 [20.0 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnsl2 armhf 1.3.0-3build3 [36.5 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgssapi-krb5-2 armhf 1.20.1-6ubuntu2 [119 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5-3 armhf 1.20.1-6ubuntu2 [321 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libk5crypto3 armhf 1.20.1-6ubuntu2 [78.6 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkrb5support0 armhf 1.20.1-6ubuntu2 [31.4 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libacl1 armhf 2.3.2-1 [15.1 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapparmor1 armhf 4.0.0-beta3-0ubuntu3 [45.1 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libblkid1 armhf 2.39.3-9ubuntu3 [160 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main armhf libcap2 armhf 1:2.66-5ubuntu1 [25.8 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main armhf libcrypt1 armhf 1:4.4.36-4 [104 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error-l10n all 1.47-3build1 [8024 B] Get:19 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error0 armhf 1.47-3build1 [61.6 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main armhf libgcrypt20 armhf 1.10.3-2 [454 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblzma5 armhf 5.6.1+really5.4.5-1build1 [112 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main armhf libzstd1 armhf 1.5.5+dfsg2-2 [265 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libkmod2 armhf 31+20240202-2ubuntu5 [45.0 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main armhf libpcre2-8-0 armhf 10.42-4ubuntu1 [198 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libselinux1 armhf 3.5-2ubuntu2 [70.9 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmount1 armhf 2.39.3-9ubuntu3 [171 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-modules-5.38 all 5.38.2-3.2build1 [3110 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdb5.3t64 armhf 5.3.28+dfsg2-6build1 [661 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm6t64 armhf 1.23-5.1build1 [30.3 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgdbm-compat4t64 armhf 1.23-5.1build1 [6216 B] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libperl5.38t64 armhf 5.38.2-3.2build1 [4109 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl armhf 5.38.2-3.2build1 [231 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-base armhf 5.38.2-3.2build1 [1671 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblocale-gettext-perl armhf 1.07-6ubuntu5 [15.1 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-iconv-perl armhf 1.7-8build3 [12.7 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-charwidth-perl armhf 0.04-11build3 [8992 B] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc6 armhf 2.39-0ubuntu8 [2828 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libc-bin armhf 2.39-0ubuntu8 [530 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssl armhf 3.0.13-0ubuntu3 [974 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main armhf libsystemd-shared armhf 255.4-1ubuntu5 [2009 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcryptsetup12 armhf 2:2.7.0-1ubuntu3 [238 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl3t64 armhf 3.0.13-0ubuntu3 [1558 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255.4-1ubuntu6 [104 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main armhf systemd-sysv armhf 255.4-1ubuntu5 [11.9 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main armhf systemd armhf 255.4-1ubuntu5 [3502 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main armhf libsystemd0 armhf 255.4-1ubuntu5 [410 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules-bin armhf 1.5.3-5ubuntu4 [47.1 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-modules armhf 1.5.3-5ubuntu4 [260 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main armhf libapt-pkg6.0t64 armhf 2.7.14 [986 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnettle8t64 armhf 3.9.1-2.2build1 [187 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libhogweed6t64 armhf 3.9.1-2.2build1 [187 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main armhf libp11-kit0 armhf 0.25.3-4ubuntu1 [258 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main armhf libunistring5 armhf 1.1-2 [512 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30t64 armhf 3.8.3-1.1ubuntu3 [947 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main armhf apt armhf 2.7.14 [1368 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main armhf apt-utils armhf 2.7.14 [210 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bzip2 armhf 1.0.8-5.1 [33.5 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbz2-1.0 armhf 1.0.8-5.1 [31.1 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g armhf 1:1.3.dfsg-3.1ubuntu2 [49.2 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main armhf debconf-i18n all 1.5.86 [205 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main armhf debconf all 1.5.86 [124 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam0g armhf 1.5.3-5ubuntu4 [62.0 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libseccomp2 armhf 2.5.5-1ubuntu3 [49.5 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main armhf libargon2-1 armhf 0~20190702+dfsg-4 [22.3 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main armhf libudev1 armhf 255.4-1ubuntu5 [166 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdevmapper1.02.1 armhf 2:1.02.185-3ubuntu3 [135 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libuuid1 armhf 2.39.3-9ubuntu3 [34.5 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfdisk1 armhf 2.39.3-9ubuntu3 [196 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main armhf mount armhf 2.39.3-9ubuntu3 [133 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcom-err2 armhf 1.47.0-2.4~exp1ubuntu3 [21.9 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main armhf libkeyutils1 armhf 1.6.3-3 [8120 B] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtirpc3t64 armhf 1.3.4+ds-1.1build1 [73.3 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main armhf linux-libc-dev armhf 6.8.0-20.20 [1555 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-14-base armhf 14-20240330-1ubuntu2 [47.4 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-s1 armhf 14-20240330-1ubuntu2 [41.5 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main armhf base-files armhf 13ubuntu9 [73.4 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debianutils armhf 5.17build1 [89.0 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bash armhf 5.2.21-2ubuntu4 [668 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdutils armhf 1:2.39.3-9ubuntu3 [102 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main armhf coreutils armhf 9.4-3ubuntu5 [1280 kB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++6 armhf 14-20240330-1ubuntu2 [714 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main armhf libxxhash0 armhf 0.8.2-2 [31.3 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main armhf libffi8 armhf 3.4.6-1 [21.0 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main armhf libidn2-0 armhf 2.3.7-2 [96.1 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdebconfclient0 armhf 0.271ubuntu3 [10.9 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main armhf base-passwd armhf 3.6.3 [51.0 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsqlite3-0 armhf 3.45.1-1ubuntu2 [590 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg armhf 2.4.4-2ubuntu16 [524 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpg-agent armhf 2.4.4-2ubuntu16 [235 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgconf armhf 2.4.4-2ubuntu16 [115 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main armhf readline-common all 8.2-4build1 [56.5 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main armhf libncursesw6 armhf 6.4+20240113-1ubuntu1 [118 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main armhf libtinfo6 armhf 6.4+20240113-1ubuntu1 [90.5 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libreadline8t64 armhf 8.2-4build1 [129 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main armhf pinentry-curses armhf 1.2.1-3ubuntu4 [36.7 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main armhf init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnpth0t64 armhf 1.6-3.1build1 [6998 B] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gpgv armhf 2.4.4-2ubuntu16 [224 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main armhf tar armhf 1.35+dfsg-3 [236 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.6ubuntu6 [1230 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dash armhf 0.5.12-6ubuntu5 [80.8 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main armhf diffutils armhf 1:3.10-1 [167 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main armhf grep armhf 3.11-4 [166 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main armhf gzip armhf 1.12-1ubuntu2 [95.8 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main armhf hostname armhf 3.23+nmu2ubuntu1 [10.3 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main armhf login armhf 1:4.13+dfsg1-4ubuntu1 [200 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main armhf ncurses-bin armhf 6.4+20240113-1ubuntu1 [178 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main armhf sed armhf 4.9-2 [198 kB] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main armhf util-linux armhf 2.39.3-9ubuntu3 [1216 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main armhf ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main armhf sysvinit-utils armhf 3.08-6ubuntu2 [33.7 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main armhf logsave armhf 1.47.0-2.4~exp1ubuntu3 [21.9 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libext2fs2t64 armhf 1.47.0-2.4~exp1ubuntu3 [201 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main armhf e2fsprogs armhf 1.47.0-2.4~exp1ubuntu3 [571 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main armhf optipng armhf 0.7.8+ds-1build2 [109 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpng16-16t64 armhf 1.6.43-5build1 [166 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main armhf init armhf 1.66ubuntu1 [6186 B] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsmartcols1 armhf 2.39.3-9ubuntu3 [117 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf uuid-runtime armhf 2.39.3-9ubuntu3 [41.8 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main armhf libattr1 armhf 1:2.5.2-1 [10.3 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main armhf libaudit-common all 1:3.1.2-2.1 [5674 B] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcap-ng0 armhf 0.8.4-2build2 [13.6 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main armhf libmd0 armhf 1.1.0-2 [23.1 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage-common all 3.5-1build4 [10.1 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main armhf libsepol2 armhf 3.5-2 [262 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage2 armhf 3.5-1build4 [84.5 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main armhf passwd armhf 1:4.13+dfsg1-4ubuntu1 [817 kB] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libproc2-0 armhf 2:4.0.4-4ubuntu3 [49.0 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libss2 armhf 1.47.0-2.4~exp1ubuntu3 [14.7 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main armhf mawk armhf 1.3.4.20240123-1 [115 kB] Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main armhf procps armhf 2:4.0.4-4ubuntu3 [700 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main armhf sensible-utils all 0.0.22 [22.5 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main armhf ca-certificates all 20240203 [159 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main armhf krb5-locales all 1.20.1-6ubuntu1 [13.8 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main armhf tzdata all 2024a-1ubuntu1 [273 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main armhf bash-completion all 1:2.11-8 [180 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main armhf bsdextrautils armhf 2.39.3-9ubuntu3 [78.7 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgpm2 armhf 1.20.7-11 [13.6 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main armhf libip4tc2 armhf 1.8.10-3ubuntu1 [21.2 kB] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libjansson4 armhf 2.14-2build2 [28.2 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main armhf psmisc armhf 23.7-1build1 [176 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main armhf xz-utils armhf 5.6.1+really5.4.5-1build1 [267 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main armhf libctf0 armhf 2.42-4ubuntu2 [87.7 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main armhf libctf-nobfd0 armhf 2.42-4ubuntu2 [88.0 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main armhf binutils-arm-linux-gnueabihf armhf 2.42-4ubuntu2 [2925 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main armhf libbinutils armhf 2.42-4ubuntu2 [460 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main armhf binutils armhf 2.42-4ubuntu2 [3072 B] Get:150 http://ftpmaster.internal/ubuntu noble/main armhf binutils-common armhf 2.42-4ubuntu2 [217 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main armhf libsframe1 armhf 2.42-4ubuntu2 [13.1 kB] Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libubsan1 armhf 14-20240330-1ubuntu2 [1153 kB] Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgomp1 armhf 14-20240330-1ubuntu2 [125 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libatomic1 armhf 14-20240330-1ubuntu2 [7846 B] Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libasan8 armhf 14-20240330-1ubuntu2 [2940 kB] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main armhf g++-13 armhf 13.2.0-23ubuntu3 [14.5 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13 armhf 13.2.0-23ubuntu3 [450 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++-13-dev armhf 13.2.0-23ubuntu3 [2455 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-13-dev armhf 13.2.0-23ubuntu3 [899 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcc1-0 armhf 14-20240330-1ubuntu2 [39.1 kB] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cpp-13 armhf 13.2.0-23ubuntu3 [1034 B] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-base armhf 13.2.0-23ubuntu3 [48.6 kB] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu3 [16.8 MB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main armhf g++-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu3 [9939 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main armhf cpp-13-arm-linux-gnueabihf armhf 13.2.0-23ubuntu3 [8759 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main armhf g++ armhf 4:13.2.0-7ubuntu1 [1090 B] Get:167 http://ftpmaster.internal/ubuntu noble/main armhf gcc armhf 4:13.2.0-7ubuntu1 [5022 B] Get:168 http://ftpmaster.internal/ubuntu noble/main armhf cpp armhf 4:13.2.0-7ubuntu1 [22.4 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main armhf cpp-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [5320 B] Get:170 http://ftpmaster.internal/ubuntu noble/main armhf gcc-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [1220 B] Get:171 http://ftpmaster.internal/ubuntu noble/main armhf g++-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [966 B] Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main armhf lto-disabled-list all 47 [12.4 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main armhf libfakeroot armhf 1.33-1 [28.7 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main armhf fakeroot armhf 1.33-1 [68.6 kB] Preconfiguring packages ... 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Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.1build1) ... Preparing to unpack .../5-linux-libc-dev_6.8.0-20.20_armhf.deb ... Unpacking linux-libc-dev:armhf (6.8.0-20.20) over (6.5.0-9.9) ... Selecting previously unselected package gcc-14-base:armhf. Preparing to unpack .../6-gcc-14-base_14-20240330-1ubuntu2_armhf.deb ... Unpacking gcc-14-base:armhf (14-20240330-1ubuntu2) ... Setting up gcc-14-base:armhf (14-20240330-1ubuntu2) ... (Reading database ... 14977 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14-20240330-1ubuntu2_armhf.deb ... Unpacking libgcc-s1:armhf (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Setting up libgcc-s1:armhf (14-20240330-1ubuntu2) ... 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Universal Time is now: Sun Mar 31 19:06:17 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... Setting up gcc-13-base:armhf (13.2.0-23ubuntu3) ... Setting up bash-completion (1:2.11-8) ... Setting up xz-utils (5.6.1+really5.4.5-1build1) ... Setting up perl-modules-5.38 (5.38.2-3.2build1) ... Setting up libproc2-0:armhf (2:4.0.4-4ubuntu3) ... Setting up libpng16-16t64:armhf (1.6.43-5build1) ... Setting up libatomic1:armhf (14-20240330-1ubuntu2) ... Setting up libss2:armhf (1.47.0-2.4~exp1ubuntu3) ... Setting up libncursesw6:armhf (6.4+20240113-1ubuntu1) ... Setting up libk5crypto3:armhf (1.20.1-6ubuntu2) ... Setting up logsave (1.47.0-2.4~exp1ubuntu3) ... Setting up libdb5.3t64:armhf (5.3.28+dfsg2-6build1) ... Setting up libubsan1:armhf (14-20240330-1ubuntu2) ... Setting up sensible-utils (0.0.22) ... Setting up uuid-runtime (2.39.3-9ubuntu3) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. 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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 (5.38.2-3.2build1) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up libgssapi-krb5-2:armhf (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu6) ... Setting up libreadline8t64:armhf (8.2-4build1) ... Setting up libgcc-13-dev:armhf (13.2.0-23ubuntu3) ... Setting up gpgconf (2.4.4-2ubuntu16) ... Setting up libc6-dev:armhf (2.39-0ubuntu8) ... Setting up binutils-arm-linux-gnueabihf (2.42-4ubuntu2) ... Setting up gpg (2.4.4-2ubuntu16) ... Setting up cpp-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... Setting up libstdc++-13-dev:armhf (13.2.0-23ubuntu3) ... Setting up gpg-agent (2.4.4-2ubuntu16) ... Setting up cpp-13 (13.2.0-23ubuntu3) ... Setting up libtirpc3t64:armhf (1.3.4+ds-1.1build1) ... Setting up binutils (2.42-4ubuntu2) ... Setting up gcc-13-arm-linux-gnueabihf (13.2.0-23ubuntu3) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:armhf (1.3.4+ds-1.1build1) ... Setting up gcc-13 (13.2.0-23ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:armhf (1.3.0-3build3) ... Setting up gcc-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... Setting up g++-13-arm-linux-gnueabihf (13.2.0-23ubuntu3) ... Setting up g++-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu3) ... Setting up libnss-nisplus:armhf (1.3-5) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:armhf (1.3.0-3build3) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15022 files and directories currently installed.) Purging configuration files for libssl3:armhf (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-27988872 armhf noble-proposed -c chroot:build-PACKAGEBUILD-27988872 --arch=armhf --dist=noble-proposed --nolog htslib_1.19+ds-1.1build3.dsc Initiating build PACKAGEBUILD-27988872 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos03-arm64-021.buildd +==============================================================================+ | htslib 1.19+ds-1.1build3 (armhf) Sun, 31 Mar 2024 19:06:25 +0000 | +==============================================================================+ Package: htslib Version: 1.19+ds-1.1build3 Source Version: 1.19+ds-1.1build3 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27988872/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/htslib-5b9FID/resolver-BxRvKc' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- htslib_1.19+ds-1.1build3.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/htslib-5b9FID/htslib-1.19+ds' with '<>' I: NOTICE: Log filtering will replace 'build/htslib-5b9FID' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0), build-essential, fakeroot Filtered Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0), build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [434 B] Get:5 copy:/<>/apt_archive ./ Packages [515 B] Fetched 1906 B in 0s (80.4 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 ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libelf1t64 libfile-stripnondeterminism-perl libhtscodecs-dev libhtscodecs2 libicu74 libldap2 liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libpipeline1 libpsl5t64 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbz2-dev libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libelf1t64 libfile-stripnondeterminism-perl libhtscodecs-dev libhtscodecs2 libicu74 libldap2 liblzma-dev libmagic-mgc libmagic1t64 libnghttp2-14 libpipeline1 libpsl5t64 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 49 newly installed, 0 to remove and 1 not upgraded. Need to get 26.1 MB of archives. After this operation, 81.8 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [736 B] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libelf1t64 armhf 0.190-1.1build3 [49.9 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main armhf libicu74 armhf 74.2-1ubuntu1 [10.5 MB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libxml2 armhf 2.9.14+dfsg-1.3ubuntu3 [595 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic-mgc armhf 1:5.45-3build1 [307 kB] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libmagic1t64 armhf 1:5.45-3build1 [81.4 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf file armhf 1:5.45-3build1 [21.1 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main armhf gettext-base armhf 0.21-14ubuntu1 [38.0 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libuchardet0 armhf 0.0.8-1 [73.9 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main armhf groff-base armhf 1.23.0-3build2 [946 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libnghttp2-14 armhf 1.59.0-1build2 [68.1 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpipeline1 armhf 1.5.7-2 [26.2 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libpsl5t64 armhf 0.21.2-1.1build1 [55.8 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf man-db armhf 2.12.0-4build1 [1202 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main armhf m4 armhf 1.4.19-4 [235 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main armhf autoconf all 2.71-3 [339 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main armhf autotools-dev all 20220109.1 [44.9 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main armhf automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main armhf autopoint all 0.21-14ubuntu1 [422 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main armhf libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main armhf libtool all 2.4.7-7 [166 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main armhf dh-autoreconf all 20 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main armhf libsub-override-perl all 0.10-1 [10.0 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main armhf dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdw1t64 armhf 0.190-1.1build3 [235 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debugedit armhf 1:5.0-5build1 [42.2 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main armhf dwz armhf 0.15-1build5 [116 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main armhf gettext armhf 0.21-14ubuntu1 [800 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main armhf intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main armhf po-debconf all 1.0.21+nmu1 [233 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main armhf debhelper all 13.14.1ubuntu5 [869 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main armhf libbrotli1 armhf 1.1.0-2build1 [319 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libbz2-dev armhf 1.0.8-5.1 [30.5 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-5ubuntu2 [19.1 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsasl2-2 armhf 2.1.28+dfsg1-5ubuntu2 [49.7 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main armhf libldap2 armhf 2.6.7+dfsg-1~exp1ubuntu6 [172 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build7 [51.3 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main armhf libssh-4 armhf 0.10.6-2build1 [169 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main armhf libcurl3t64-gnutls armhf 8.5.0-2ubuntu8 [290 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main armhf libcurl4-gnutls-dev armhf 8.5.0-2ubuntu8 [408 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1 [41.3 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate-dev armhf 1.19-1 [48.4 kB] Get:45 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs2 armhf 1.6.0-1 [65.9 kB] Get:46 http://ftpmaster.internal/ubuntu noble/universe armhf libhtscodecs-dev armhf 1.6.0-1 [2956 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl-dev armhf 3.0.13-0ubuntu3 [2084 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g-dev armhf 1:1.3.dfsg-3.1ubuntu2 [880 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblzma-dev armhf 5.6.1+really5.4.5-1build1 [165 kB] Preconfiguring packages ... Fetched 26.1 MB in 2s (14.5 MB/s) Selecting previously unselected package libelf1t64:armhf. (Reading database ... 15022 files and directories currently installed.) Preparing to unpack .../00-libelf1t64_0.190-1.1build3_armhf.deb ... Unpacking libelf1t64:armhf (0.190-1.1build3) ... Selecting previously unselected package libicu74:armhf. Preparing to unpack .../01-libicu74_74.2-1ubuntu1_armhf.deb ... Unpacking libicu74:armhf (74.2-1ubuntu1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.3ubuntu3_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3ubuntu3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3build1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3build1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3build1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3build1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3build1_armhf.deb ... Unpacking file (1:5.45-3build1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14ubuntu1_armhf.deb ... Unpacking gettext-base (0.21-14ubuntu1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../07-libuchardet0_0.0.8-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-3build2_armhf.deb ... Unpacking groff-base (1.23.0-3build2) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../09-libnghttp2-14_1.59.0-1build2_armhf.deb ... Unpacking libnghttp2-14:armhf (1.59.0-1build2) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../10-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package libpsl5t64:armhf. Preparing to unpack .../11-libpsl5t64_0.21.2-1.1build1_armhf.deb ... Unpacking libpsl5t64:armhf (0.21.2-1.1build1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.12.0-4build1_armhf.deb ... Unpacking man-db (2.12.0-4build1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... Unpacking automake (1:1.16.5-1.3ubuntu1) ... Selecting previously unselected package autopoint. 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Preparing to unpack .../23-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 .../24-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libdw1t64:armhf. Preparing to unpack .../25-libdw1t64_0.190-1.1build3_armhf.deb ... Unpacking libdw1t64:armhf (0.190-1.1build3) ... Selecting previously unselected package debugedit. Preparing to unpack .../26-debugedit_1%3a5.0-5build1_armhf.deb ... Unpacking debugedit (1:5.0-5build1) ... Selecting previously unselected package dwz. Preparing to unpack .../27-dwz_0.15-1build5_armhf.deb ... Unpacking dwz (0.15-1build5) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-14ubuntu1_armhf.deb ... Unpacking gettext (0.21-14ubuntu1) ... Selecting previously unselected package intltool-debian. 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Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../35-libsasl2-2_2.1.28+dfsg1-5ubuntu2_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu2) ... Selecting previously unselected package libldap2:armhf. Preparing to unpack .../36-libldap2_2.6.7+dfsg-1~exp1ubuntu6_armhf.deb ... Unpacking libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../37-librtmp1_2.4+20151223.gitfa8646d.1-2build7_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build7) ... Selecting previously unselected package libssh-4:armhf. Preparing to unpack .../38-libssh-4_0.10.6-2build1_armhf.deb ... Unpacking libssh-4:armhf (0.10.6-2build1) ... Selecting previously unselected package libcurl3t64-gnutls:armhf. Preparing to unpack .../39-libcurl3t64-gnutls_8.5.0-2ubuntu8_armhf.deb ... Unpacking libcurl3t64-gnutls:armhf (8.5.0-2ubuntu8) ... 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Unpacking libssl-dev:armhf (3.0.13-0ubuntu3) ... Selecting previously unselected package zlib1g-dev:armhf. Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg-3.1ubuntu2_armhf.deb ... Unpacking zlib1g-dev:armhf (1:1.3.dfsg-3.1ubuntu2) ... Selecting previously unselected package liblzma-dev:armhf. Preparing to unpack .../47-liblzma-dev_5.6.1+really5.4.5-1build1_armhf.deb ... Unpacking liblzma-dev:armhf (5.6.1+really5.4.5-1build1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../48-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:armhf (1.6.0-1) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libmagic-mgc (1:5.45-3build1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.14.1ubuntu5) ... Setting up libbrotli1:armhf (1.1.0-2build1) ... Setting up libmagic1t64:armhf (1:5.45-3build1) ... Setting up libpsl5t64:armhf (0.21.2-1.1build1) ... Setting up libnghttp2-14:armhf (1.59.0-1build2) ... Setting up libdeflate0:armhf (1.19-1) ... Setting up gettext-base (0.21-14ubuntu1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3build1) ... Setting up libelf1t64:armhf (0.190-1.1build3) ... Setting up libdw1t64:armhf (0.190-1.1build3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-5ubuntu2) ... Setting up libhtscodecs-dev:armhf (1.6.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build7) ... Setting up libssl-dev:armhf (3.0.13-0ubuntu3) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-5ubuntu2) ... Setting up libssh-4:armhf (0.10.6-2build1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:armhf (5.6.1+really5.4.5-1build1) ... Setting up libicu74:armhf (74.2-1ubuntu1) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg-3.1ubuntu2) ... Setting up dwz (0.15-1build5) ... Setting up libuchardet0:armhf (0.0.8-1) ... Setting up debugedit (1:5.0-5build1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libdeflate-dev:armhf (1.19-1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3ubuntu3) ... Setting up libldap2:armhf (2.6.7+dfsg-1~exp1ubuntu6) ... Setting up libbz2-dev:armhf (1.0.8-5.1) ... 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 libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libtool (2.4.7-7) ... Setting up libcurl3t64-gnutls:armhf (8.5.0-2ubuntu8) ... Setting up libcurl4-gnutls-dev:armhf (8.5.0-2ubuntu8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3build2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-4build1) ... 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 debhelper (13.14.1ubuntu5) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 arm64 (armv7l) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu3 gcc-13_13.2.0-23ubuntu3 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 linux-libc-dev_6.8.0-20.20 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.14 apt-utils_2.7.14 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu9 base-passwd_3.6.3 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-arm-linux-gnueabihf_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu3 bsdutils_1:2.39.3-9ubuntu3 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3ubuntu5 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu3 cpp-13-arm-linux-gnueabihf_13.2.0-23ubuntu3 cpp-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.6ubuntu6 dpkg-dev_1.22.6ubuntu6 dwz_0.15-1build5 e2fsprogs_1.47.0-2.4~exp1ubuntu3 fakeroot_1.33-1 file_1:5.45-3build1 findutils_4.9.0-5 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-23ubuntu3 g++-13-arm-linux-gnueabihf_13.2.0-23ubuntu3 g++-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-23ubuntu3 gcc-13-arm-linux-gnueabihf_13.2.0-23ubuntu3 gcc-13-base_13.2.0-23ubuntu3 gcc-14-base_14-20240330-1ubuntu2 gcc-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 gpg_2.4.4-2ubuntu16 gpg-agent_2.4.4-2ubuntu16 gpgconf_2.4.4-2ubuntu16 gpgv_2.4.4-2ubuntu16 grep_3.11-4 groff-base_1.23.0-3build2 gzip_1.12-1ubuntu2 hostname_3.23+nmu2ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-6ubuntu1 libacl1_2.3.2-1 libapparmor1_4.0.0-beta3-0ubuntu3 libapt-pkg6.0t64_2.7.14 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240330-1ubuntu2 libassuan0_2.5.6-1 libatomic1_14-20240330-1ubuntu2 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.1-1 libbinutils_2.42-4ubuntu2 libblkid1_2.39.3-9ubuntu3 libbrotli1_1.1.0-2build1 libbz2-1.0_1.0.8-5.1 libbz2-dev_1.0.8-5.1 libc-bin_2.39-0ubuntu8 libc-dev-bin_2.39-0ubuntu8 libc6_2.39-0ubuntu8 libc6-dev_2.39-0ubuntu8 libcap-ng0_0.8.4-2build2 libcap2_1:2.66-5ubuntu1 libcc1-0_14-20240330-1ubuntu2 libcom-err2_1.47.0-2.4~exp1ubuntu3 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.7.0-1ubuntu3 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libcurl3t64-gnutls_8.5.0-2ubuntu8 libcurl4-gnutls-dev_8.5.0-2ubuntu8 libdb5.3t64_5.3.28+dfsg2-6build1 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdeflate-dev_1.19-1 libdeflate0_1.19-1 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdpkg-perl_1.22.6ubuntu6 libdw1t64_0.190-1.1build3 libelf1t64_0.190-1.1build3 libext2fs2t64_1.47.0-2.4~exp1ubuntu3 libfakeroot_1.33-1 libfdisk1_2.39.3-9ubuntu3 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-23ubuntu3 libgcc-s1_14-20240330-1ubuntu2 libgcrypt20_1.10.3-2 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30t64_3.8.3-1.1ubuntu3 libgomp1_14-20240330-1ubuntu2 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-11 libgssapi-krb5-2_1.20.1-6ubuntu2 libhogweed6t64_3.9.1-2.2build1 libhtscodecs-dev_1.6.0-1 libhtscodecs2_1.6.0-1 libicu74_74.2-1ubuntu1 libidn2-0_2.3.7-2 libip4tc2_1.8.10-3ubuntu1 libisl23_0.26-3 libjansson4_2.14-2build2 libjson-c5_0.17-1 libk5crypto3_1.20.1-6ubuntu2 libkeyutils1_1.6.3-3 libkmod2_31+20240202-2ubuntu5 libkrb5-3_1.20.1-6ubuntu2 libkrb5support0_1.20.1-6ubuntu2 libldap2_2.6.7+dfsg-1~exp1ubuntu6 liblocale-gettext-perl_1.07-6ubuntu5 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.4-1 liblzma-dev_5.6.1+really5.4.5-1build1 liblzma5_5.6.1+really5.4.5-1build1 libmagic-mgc_1:5.45-3build1 libmagic1t64_1:5.45-3build1 libmd0_1.1.0-2 libmount1_2.39.3-9ubuntu3 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20240113-1ubuntu1 libnettle8t64_3.9.1-2.2build1 libnghttp2-14_1.59.0-1build2 libnpth0t64_1.6-3.1build1 libnsl-dev_1.3.0-3build3 libnsl2_1.3.0-3build3 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-5 libp11-kit0_0.25.3-4ubuntu1 libpam-modules_1.5.3-5ubuntu4 libpam-modules-bin_1.5.3-5ubuntu4 libpam-runtime_1.5.3-5ubuntu4 libpam0g_1.5.3-5ubuntu4 libpcre2-8-0_10.42-4ubuntu1 libperl5.38t64_5.38.2-3.2build1 libpipeline1_1.5.7-2 libpng16-16t64_1.6.43-5build1 libproc2-0_2:4.0.4-4ubuntu3 libpsl5t64_0.21.2-1.1build1 libreadline8t64_8.2-4build1 librtmp1_2.4+20151223.gitfa8646d.1-2build7 libsasl2-2_2.1.28+dfsg1-5ubuntu2 libsasl2-modules-db_2.1.28+dfsg1-5ubuntu2 libseccomp2_2.5.5-1ubuntu3 libselinux1_3.5-2ubuntu2 libsemanage-common_3.5-1build4 libsemanage2_3.5-1build4 libsepol2_3.5-2 libsframe1_2.42-4ubuntu2 libsmartcols1_2.39.3-9ubuntu3 libsqlite3-0_3.45.1-1ubuntu2 libss2_1.47.0-2.4~exp1ubuntu3 libssh-4_0.10.6-2build1 libssl-dev_3.0.13-0ubuntu3 libssl3t64_3.0.13-0ubuntu3 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 libsub-override-perl_0.10-1 libsystemd-shared_255.4-1ubuntu5 libsystemd0_255.4-1ubuntu5 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11build3 libtext-iconv-perl_1.7-8build3 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20240113-1ubuntu1 libtirpc-common_1.3.4+ds-1.1build1 libtirpc-dev_1.3.4+ds-1.1build1 libtirpc3t64_1.3.4+ds-1.1build1 libtool_2.4.7-7 libubsan1_14-20240330-1ubuntu2 libuchardet0_0.0.8-1 libudev1_255.4-1ubuntu5 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-9ubuntu3 libxml2_2.9.14+dfsg-1.3ubuntu3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.0-20.20 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-4ubuntu1 logsave_1.47.0-2.4~exp1ubuntu3 lto-disabled-list_47 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-4build1 mawk_1.3.4.20240123-1 mount_2.39.3-9ubuntu3 ncurses-base_6.4+20240113-1ubuntu1 ncurses-bin_6.4+20240113-1ubuntu1 openssl_3.0.13-0ubuntu3 optipng_0.7.8+ds-1build2 passwd_1:4.13+dfsg1-4ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3.2build1 perl-base_5.38.2-3.2build1 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-3.2build1 pinentry-curses_1.2.1-3ubuntu4 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-4ubuntu3 psmisc_23.7-1build1 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 systemd_255.4-1ubuntu5 systemd-dev_255.4-1ubuntu6 systemd-sysv_255.4-1ubuntu5 sysvinit-utils_3.08-6ubuntu2 tar_1.35+dfsg-3 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-9ubuntu3 uuid-runtime_2.39.3-9ubuntu3 xz-utils_5.6.1+really5.4.5-1build1 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: htslib Binary: libhts3t64, libhts-dev, htslib-test, tabix Architecture: any all Version: 1.19+ds-1.1build3 Maintainer: Ubuntu Developers Uploaders: Charles Plessy , Andreas Tille , Michael R. Crusoe , Steffen Moeller , Étienne Mollier Homepage: https://github.com/samtools/htslib Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/htslib Vcs-Git: https://salsa.debian.org/med-team/htslib.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, build-essential Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0) Package-List: htslib-test deb science optional arch=all libhts-dev deb libdevel optional arch=any libhts3t64 deb libs optional arch=any tabix deb science optional arch=any Checksums-Sha1: 33b65ea5de06a41c42cf8ef0d74f7ef7e4739408 1522390 htslib_1.19+ds.orig.tar.bz2 82a8183deb3e8fc927d8afe7255d4063f2ff4db6 21420 htslib_1.19+ds-1.1build3.debian.tar.xz Checksums-Sha256: e740e5a68db806a4c8252009348da5f0cc1bcdd134f702e4e1cce724e855f777 1522390 htslib_1.19+ds.orig.tar.bz2 37ebea6ed0e05d77181265ace97b1ee646127a6ef613a33faa1d3b8f50295d27 21420 htslib_1.19+ds-1.1build3.debian.tar.xz Files: 79efd7a83fdd5a36a3d8057180681ec0 1522390 htslib_1.19+ds.orig.tar.bz2 46b8056d01f089f97e8fd8c6494d52fd 21420 htslib_1.19+ds-1.1build3.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQJOBAEBCgA4FiEErEg/aN5yj0PyIC/KVo0w8yGyEz0FAmYJqrcaHHN0ZXZlLmxh bmdhc2VrQHVidW50dS5jb20ACgkQVo0w8yGyEz1D1Q//Qg6GHX0MdVYYhcXvD+TN 3XjqBXXhPqBHSfLrIuJvpDdyomsxxmNZa46ZIBuhgsJbecAug+AdnKQn/5V88B98 1V+4TQZDhYKV1Oh5ijUukOdiTNMWDFA91OqbW2dCLmE3qVa/K87IrYItwlUw8Nwp PsKx8Ck5aSfbqXJkxM1P9Ji282N13rJ7EMge7kO7h2JuFatCp59oNqRE1RIjw9pi Q+wFO/tAJ1NPJ7B1JZcHL/pI7mERI6gwV1tiP1dPW+cB+4A5Y7luiP0EkZ1cxcsV wIHLHuqajHzAYsr3TGPPy91xMOsMNkfm1QBJ+SekIK6F93/7Y+ygHwXaZbNjj9mo ejtC0UdQp3fVzLEmH2p8VRnpGDv5jwDMmu6bjA1VGvrxoIuKrH9L59hGaqdkCCtp rlSkFSbhhEtmSKeyybOFEsn1pu5H7zSQ8LbtqQSQMyPlxnHgexUKjfAmiXwXJ5Lv 0UDu12M9fjfc0sLVgnXV+oZPl6daKb7/Tp2rvYSkXH4azRJoWRkYIPcpmwKPcJI8 bA9TLhZtviHa8652ixs4FeHP6Vmo8D1CUxUI18SOapTWX13WLn/ucTBOtjNpchyh fPKXKtJOf/ckFxEi3aUmvRIF69OXWndBhnkxiZ24/TzdpxAbPl+b5/bWjdUQynXX w48Q3I/kjQOTA9gpbf+7vxU= =ULfj -----END PGP SIGNATURE----- gpgv: Signature made Sun Mar 31 18:25:59 2024 UTC gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./htslib_1.19+ds-1.1build3.dsc: no acceptable signature found dpkg-source: info: extracting htslib in /<> dpkg-source: info: unpacking htslib_1.19+ds.orig.tar.bz2 dpkg-source: info: unpacking htslib_1.19+ds-1.1build3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_git_version dpkg-source: info: applying define_PATH_MAX.patch dpkg-source: info: applying fPIC.patch dpkg-source: info: applying testShebang.patch dpkg-source: info: applying fix_float_precision dpkg-source: info: applying cram_to_bam_export.patch dpkg-source: info: applying fix_sequence_of_linked_libs.patch dpkg-source: info: applying trim-file-prefix.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-27988872 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27988872 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27988872 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 -B -rfakeroot dpkg-buildpackage: info: source package htslib dpkg-buildpackage: info: source version 1.19+ds-1.1build3 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from htslib-1.19+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j4 distclean make[2]: Entering directory '/<>' rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* test/faidx/FAIL* \ test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* \ header-exports.txt shlib-exports-so.txt rm -f libhts.so libhts.so.* rm -rf htscodecs/tests/test.out rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM config_vars.h version.h rm -f htscodecs/htscodecs/*.o htscodecs/htscodecs/*.pico rm -f hts-object-files rm -f htscodecs/tests/*.o rm -f libhts.a annot-tsv bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/pileup_mod test/plugins-dlhts test/sam test/test_bgzf test/test_expr test/test_faidx test/test_kfunc test/test_kstring test/test_mod test/test_realn test/test-regidx test/test_str2int test/test_time_funcs test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/test_introspection test/test-bcf_set_variant_type test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7 rm -f htscodecs/tests/rans4x8 htscodecs/tests/rans4x16pr htscodecs/tests/arith_dynamic htscodecs/tests/tokenise_name3 htscodecs/tests/fqzcomp_qual htscodecs/tests/varint rm -f config.cache config.h config.log config.mk config.status rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk htscodecs.mk rm -rf autom4te.cache make[2]: Leaving directory '/<>' rm -rf test_backup/ make[1]: Leaving directory '/<>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/htslib-test.substvars debian/tabix.substvars debian/files rm -fr -- debian/libhts3t64/ debian/tmp/ debian/libhts-dev/ debian/htslib-test/ debian/tabix/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch dh_update_autotools_config -a cp -an --reflink=auto config.guess debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3.tmp cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead mv debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3.tmp debian/.debhelper/bucket/files/ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3 cp -f /usr/share/misc/config.guess ./config.guess cp -an --reflink=auto config.sub debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b.tmp cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead mv debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b.tmp debian/.debhelper/bucket/files/465c5fe67c7d36b72e808812716445d4d38d4b94734ca8d36a8639d12323878b cp -f /usr/share/misc/config.sub ./config.sub dh_autoreconf -a find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' # create clean copy of test dir cp -a test test_backup # to help with cross building, otherwise MMAP might get turned off export ac_cv_func_mmap_fixed_mapped=yes \ && autoconf \ && dh_auto_configure -- \ --enable-libcurl \ --enable-gcs \ --enable-s3 \ --enable-plugins \ --with-plugin-dir='/usr/lib/arm-linux-gnueabihf/htslib' \ --with-external-htscodecs \ --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/arm-linux-gnueabihf/htslib' ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/usr/lib/arm-linux-gnueabihf/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/arm-linux-gnueabihf/htslib checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for gcc options needed to detect all undeclared functions... none needed checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for sse4.1... none checking C compiler flags needed for avx2... none checking C compiler flags needed for avx512f... none checking for pkg-config... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... yes checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf checking for getpagesize... yes checking for working mmap... (cached) yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing dlsym... none required checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking for htscodecs/rANS_static4x16.h... yes checking for rans_compress_bound_4x16 in -lhtscodecs... yes checking for libdeflate.h... yes checking for libdeflate_deflate_compress in -ldeflate... yes checking for curl/curl.h... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... -lcrypto checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_external.mk to htscodecs.mk make[1]: Leaving directory '/<>' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_build-arch make[1]: Entering directory '/<>' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.19" \ libdir=/usr/lib/arm-linux-gnueabihf make -j4 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3" PACKAGE_VERSION=1.19 libdir=/usr/lib/arm-linux-gnueabihf make[2]: Entering directory '/<>' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kfunc.o kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kstring.o kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzf.o bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o errmod.o errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o faidx.o faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o header.o header.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.19"' > version.h printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \ 'gcc' \ '-I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3' \ '-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects' \ '-Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic' \ '-ldeflate -lhtscodecs -llzma -lbz2 -lz -lm ' \ | sed 's/-ffile-prefix-map=[^ ]*=.//' \ > config_vars.h gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_expr.o hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_os.o hts_os.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o md5.o md5.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o multipart.o multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o probaln.o probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o realn.o realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o regidx.o regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o region.o region.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam.o sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_mods.o sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tbx.o tbx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o textutils.o textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o thread_pool.o thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf.o vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcfutils.o vcfutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/arm-linux-gnueabihf/htslib\" -c -o plugin.o plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kfunc.pico kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kstring.pico kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o bgzf.pico bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o errmod.pico errmod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security 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-Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile.pico hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts.pico hts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts_expr.pico hts_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security 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-D_FORTIFY_SOURCE=3 -fPIC -c -o multipart.pico multipart.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o probaln.pico probaln.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o realn.pico realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security 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-Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam.pico sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam_mods.pico sam_mods.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat 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-D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o textutils.pico textutils.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o thread_pool.pico thread_pool.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcf.pico vcf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. 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-I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection 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-Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/arm-linux-gnueabihf/htslib\" -fPIC -c -o plugin.pico plugin.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o annot-tsv.o annot-tsv.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzip.o bgzip.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o htsfile.o htsfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tabix.o tabix.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_gcs.pico hfile_gcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3.pico hfile_s3.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hts_endian.o test/hts_endian.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hfile.o test/hfile.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup.o test/pileup.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup_mod.o test/pileup_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/sam.o test/sam.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_bgzf.o test/test_bgzf.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_expr.o test/test_expr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_faidx.o test/test_faidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kfunc.o test/test_kfunc.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kstring.o test/test_kstring.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_mod.o test/test_mod.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_realn.o test/test_realn.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_str2int.o test/test_str2int.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_time_funcs.o test/test_time_funcs.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_view.o test/test_view.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_index.o test/test_index.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_introspection.o test/test_introspection.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf_set_variant_type.o test/test-bcf_set_variant_type.c sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects -I. -I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts.o hts.c gcc -shared -Wl,-soname,libhts.so.3 -Wl,-version-script,htslib.map -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico sam_mods.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico plugin.pico -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hts_endian test/hts_endian.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/plugins-dlhts test/plugins-dlhts.o -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm ln -sf libhts.so libhts.so.3 gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_time_funcs test/test_time_funcs.o gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_libcurl.so hfile_libcurl.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcurl -lpthread gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_gcs.so hfile_gcs.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3.so hfile_s3.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lpthread gcc -shared -Wl,-E -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o hfile_s3_write.so hfile_s3_write.pico libhts.so -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lcrypto -lcurl -lpthread ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o plugin.o ranlib libhts.a gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o annot-tsv annot-tsv.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o bgzip bgzip.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o htsfile htsfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o tabix tabix.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm libhts.a -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/fieldarith test/fieldarith.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/hfile test/hfile.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup test/pileup.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/pileup_mod test/pileup_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/sam test/sam.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_bgzf test/test_bgzf.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_expr test/test_expr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_faidx test/test_faidx.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kfunc test/test_kfunc.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_kstring test/test_kstring.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_mod test/test_mod.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_realn test/test_realn.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-regidx test/test-regidx.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_str2int test/test_str2int.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_view test/test_view.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_index test/test_index.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-api test/test-vcf-api.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-parse-reg test/test-parse-reg.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test_introspection test/test_introspection.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread gcc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-flto -fvisibility=hidden -ffat-lto-objects -fvisibility=hidden -rdynamic -o test/test-bcf_set_variant_type test/test-bcf_set_variant_type.o libhts.a -ldeflate -lhtscodecs -llzma -lbz2 -lz -lm -lpthread make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_test-arch make[1]: Entering directory '/<>' dh_auto_test -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.19" \ libdir=/usr/lib/arm-linux-gnueabihf \ || \ if find . -name "FAIL*" > /dev/null ; then \ for file in $(find . -name "FAIL*"); do echo ${file}; cat ${file}; done && false ; \ fi make -j4 test "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3" PACKAGE_VERSION=1.19 libdir=/usr/lib/arm-linux-gnueabihf make[2]: Entering directory '/<>' test/hts_endian test/test_expr test/test_kfunc test/test_kstring test/test_str2int test/test_time_funcs test/fieldarith test/fieldarith.sam test/hfile if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -g ./libhts.so; \ fi if test "xhfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so" != "x"; then \ HTS_PATH=. test/with-shlib.sh test/plugins-dlhts -l ./libhts.so; \ fi test/test_bgzf test/bgziptest.txt test/test-parse-reg -t test/colons.bam Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200} or {chr1}:100-200 instead Expected error: [E::hts_parse_region] Range is ambiguous. Use {chr1:100-200,chr3} or {chr1}:100-200,chr3 instead Expected error: [E::hts_parse_region] Mismatching braces in "{chr1" Expected error: [E::hts_parse_region] Unexpected string "x" after region Expected error: [E::hts_parse_region] Unexpected string "y" after region Expected error: [E::hts_parse_region] Unexpected string "chr3" after region cd test/faidx && ./test-faidx.sh faidx.tst Testing faidx... PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -e faidx.fa.expected.fai PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_line_length -e 24 trailingblank2 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 1 foo PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_iseq -e trailingblank3 3 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len -e 33 trailingblank1 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_seq_len64 -e 72 trailingblank2 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -e fastqs.fq.expected.fai PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 63 FAKE0005_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_line_length -e 144 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 1 SRR014849.203935_3 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_has_seq -e 0 absent PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_iseq -e FAKE0005_1 0 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len -e 453 FSRRS4401CM938_1 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -t faidx_seq_len64 -e 309 FSRRS4401AOV6A_4 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_fetch trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t faidx_fetch_seq64 trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i faidx.fa -f faidx.fa.tmp.fai -t fai_adjust_region trailingblank2:28-33 trailingblank3:4-5 bar:4-5 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t fai_fetch FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai -Q -t faidx_fetch_seq64 FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i fastqs.fq -f fastqs.fq.tmp.fai FAKE0006_1:4-12 FSRRS4401BE7HA_1:81-120 FAKE0010_2 SRR014849.50939_3:71-90 PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi -e ../ce.fa.fai PASS : $test_faidx -i ce.fa.tmp.gz -f ce.fa.tmp.gz.fai -g ce.fa.tmp.gz.gzi CHROMOSOME_I:5001-5125 CHROMOSOME_X:101-225 Expected passes: 25 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/sam_filter && ./filter.sh filter.tst Testing sam_filter... PASS : $tv -i 'filter=qname =~ "\.1" && cigar =~ "D"' ../ce#1000.sam PASS : $tv -i 'filter=rname=="CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=rname=~"CHROMOSOME_II"' ../ce#5b.sam PASS : $tv -i 'filter=cigar=~"D"' ../ce#1000.sam PASS : $tv -i 'filter=seq =~ "(AT){2}"' ../ce#1000.sam PASS : $tv -i 'filter=library=="x"' ../xx#rg.sam PASS : $tv -i 'filter=library!="x"' ../xx#rg.sam PASS : $tv -i 'filter=pos % 23 == 11' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=qlen/(flag*mapq+pos)>5' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=[NM]>=10 || [MD]=~"A.*A.*A"' -t4 ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=length(seq) != qlen' ../ce#5b.sam | grep -E -cv '^@' PASS : $tv -i 'filter=min(qual) >= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=max(qual) <= 20' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=avg(qual) >= 20 && avg(qual) <= 30' ../ce#1000.sam | grep -E -cv '^@' PASS : $tv -i 'filter=sclen>=20' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=rlen<50' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=qlen>100' ../realn02.sam | grep -E -v '^@' PASS : $tv -i 'filter=hclen>=4' ../c1#clip.sam | grep -E -v '^@' Expected passes: 18 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/tabix && ./test-tabix.sh tabix.tst Testing tabix... PASS : $tabix -f -p vcf vcf_file.tbi.tmp.vcf.gz PASS : $tabix vcf_file.tbi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.tbi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -C -p vcf vcf_file.csi.tmp.vcf.gz PASS : $tabix vcf_file.csi.tmp.vcf.gz 1:3000151-3000151 PASS : $tabix vcf_file.csi.tmp.vcf.gz 2:3199812-3199812 PASS : $tabix -f -p vcf large_chr.tmp.vcf.gz (must exit non-zero) PASS : $tabix -f -C -p vcf large_chr.tmp.vcf.gz PASS : $tabix large_chr.tmp.vcf.gz chr20:1-2147483647 PASS : $tabix -f -p bed bed_file.tbi.tmp.bed.gz PASS : $tabix bed_file.tbi.tmp.bed.gz Y:100200-100200 PASS : $tabix -f -p gff gff_file.tbi.tmp.gff.gz PASS : $tabix gff_file.tbi.tmp.gff.gz X:2934832-2935190 PASS : $tabix --separate-regions bed_file.tbi.tmp.bed.gz X:1100-1400 Y:100000-100550 Z:100000-100005 Expected passes: 14 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/mpileup && ./test-pileup.sh mpileup.tst Testing (m)pileup... PASS : $pileup mp_D.sam PASS : $pileup -m mp_D.sam PASS : $pileup mp_DI.sam PASS : $pileup -m mp_DI.sam PASS : $pileup mp_I.sam PASS : $pileup -m mp_I.sam PASS : $pileup mp_P.sam PASS : $pileup -m mp_P.sam PASS : $pileup mp_ID.sam PASS : $pileup -m mp_ID.sam PASS : $pileup mp_N.sam PASS : $pileup -m mp_N.sam PASS : $pileup mp_N2.sam PASS : $pileup -m mp_N2.sam PASS : $pileup c1#pad1.sam PASS : $pileup -m c1#pad1.sam PASS : $pileup c1#pad2.sam PASS : $pileup -m c1#pad2.sam PASS : $pileup c1#pad3.sam PASS : $pileup -m c1#pad3.sam PASS : $pileup -m small.bam Expected passes: 21 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/fastq && ./test-fastq.sh Testing fastq support PASS : $tview minimal.fq PASS : $tview minimal.fa PASS : $tview multiline.fq PASS : $tview multiline.fa PASS : $tview -i fastq_aux longline.fq PASS : $tview single.fq PASS : $tview single.fa PASS : $tview -i fastq_aux single.fq PASS : $tview -i fastq_aux single.fa PASS : $tview interleaved.fq PASS : $tview interleaved.fa PASS : $tview -i fastq_aux interleaved.fq PASS : $tview -i fastq_aux interleaved.fa PASS : $tview -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fq PASS : $tview -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_barcode=OX -i fastq_casava interleaved_casava.fa PASS : $tview -i fastq_casava filter_casava.fq PASS : $tview -i fastq_casava filter_casava.fa PASS : $tview -i fastq_aux r1.fq PASS : $tview -i fastq_aux r2.fq PASS : $tview -i fastq_aux r1.fa PASS : $tview -i fastq_aux r2.fa PASS : $tview -i fastq_name2 name2.fq PASS : $tview -i fastq_name2 name2.fa PASS : $tview -f minimal.sam PASS : $tview -F minimal.sam PASS : $tview -f -o fastq_aux single_aux.sam PASS : $tview -F -o fastq_aux single_aux.sam PASS : $tview -f -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -F -o fastq_aux -o fastq_rnum inter_aux.sam PASS : $tview -f -o fastq_casava inter_casava.sam PASS : $tview -f -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -F -o fastq_casava inter_casava.sam PASS : $tview -F -o fastq_barcode=OX -o fastq_casava inter_casavaOX.sam PASS : $tview -f -o fastq_casava filter_casava.sam PASS : $tview -F -o fastq_casava filter_casava.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -f -o fastq_aux -o fastq_rnum r2.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r1.sam PASS : $tview -F -o fastq_aux -o fastq_rnum r2.sam Expected passes: 41 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 cd test/base_mods && ./base-mods.sh base-mods.tst Testing base-modifications... PASS : $test_mod MM-chebi.sam PASS : $test_mod MM-double.sam PASS : $test_mod MM-multi.sam PASS : $test_mod MM-explicit.sam PASS : $test_mod -x MM-explicit.sam PASS : $test_mod -f 1 MM-explicit.sam PASS : $test_mod MM-not-all-modded.sam PASS : $pileup_mod < MM-pileup.sam PASS : $pileup_mod < MM-pileup2.sam PASS : $pileup_mod < MM-MNp.sam PASS : $pileup_mod < MM-MNf1.sam (must exit non-zero) PASS : $pileup_mod < MM-MNf2.sam (must exit non-zero) Expected passes: 12 Unexpected passes: 0 Expected failures: 0 Unexpected failures: 0 REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq (Expect trailing 'x' message for " -1,001x") [W::hts_parse_decimal] Ignoring unknown characters after -1,001[x] (Expect trailing 'k' message for "1.5e+3k") [W::hts_parse_decimal] Ignoring unknown characters after 1.5e+3[k] (Expect dropped fraction message for "12.3456k") [W::hts_parse_decimal] Discarding fractional part of 12.3456k [W::hts_parse_decimal] Discarding fractional part of 12.3456k (Expect invalid numeric message for "A") [W::hts_parse_decimal] Invalid numeric value A[truncated] (Expect invalid numeric message for "G") [W::hts_parse_decimal] Invalid numeric value G[truncated] (Expect invalid numeric message for " +/-") [W::hts_parse_decimal] Invalid numeric value +/-[truncated] (Expect invalid numeric message for " -.e+9999") [W::hts_parse_decimal] Invalid numeric value -.e+9999[truncated] test/test-regidx cd test && REF_PATH=: ./test.pl ${TEST_OPTS:-} bgzip round-trip no threads: .. ok bgzip text mode round-trip no threads: .. ok bgzip -b no threads: .. ok bgzip -b -I no threads: .. ok bgzip multifile no threads: .. ok bgzip round-trip 4 threads: .. ok bgzip text mode round-trip 4 threads: .. ok bgzip -b 4 threads: .. ok bgzip -b -I 4 threads: .. ok bgzip multifile 4 threads: .. ok test_index: /<>/test/test_view -l 0 -b -m 14 -x /tmp/k0XTRZeBY6/index.bam.csi /<>/test/index.sam > /tmp/k0XTRZeBY6/index.bam .. ok test_index: /<>/test/test_index -c /tmp/k0XTRZeBY6/index.bam .. ok test_index: /<>/test/test_view -l 0 -b -m 0 -x /tmp/k0XTRZeBY6/index.bam.bai /<>/test/index.sam > /tmp/k0XTRZeBY6/index.bam .. ok test_index: /<>/test/test_index -b /tmp/k0XTRZeBY6/index.bam .. ok test_index: /<>/test/test_view -l 0 -z -m 14 -x /tmp/k0XTRZeBY6/index.sam.gz.csi /<>/test/index.sam > /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 0 -x /tmp/k0XTRZeBY6/index.sam.gz.bai /<>/test/index.sam > /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 14 -x /tmp/k0XTRZeBY6/index.sam.gz.csi /<>/test/index_dos.sam > /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 0 -x /tmp/k0XTRZeBY6/index.sam.gz.bai /<>/test/index_dos.sam > /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -C -x /tmp/k0XTRZeBY6/index.cram.crai /<>/test/index.sam > /tmp/k0XTRZeBY6/index.cram .. ok test_index: /<>/test/test_index /tmp/k0XTRZeBY6/index.cram .. ok test_index: /<>/test/test_view -l 0 -b -m 14 -x /tmp/k0XTRZeBY6/index.bcf.csi /<>/test/index.vcf > /tmp/k0XTRZeBY6/index.bcf .. ok test_index: /<>/test/test_index -c /tmp/k0XTRZeBY6/index.bcf .. ok test_index: /<>/test/test_view -l 0 -z -m 14 -x /tmp/k0XTRZeBY6/index.vcf.gz.csi /<>/test/index.vcf > /tmp/k0XTRZeBY6/index.vcf.gz .. ok test_index: /<>/test/test_index -c /tmp/k0XTRZeBY6/index.vcf.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 0 -x /tmp/k0XTRZeBY6/index.vcf.gz.tbi /<>/test/index.vcf > /tmp/k0XTRZeBY6/index.vcf.gz .. ok test_index: /<>/test/test_index -t /tmp/k0XTRZeBY6/index.vcf.gz .. ok test_index: /<>/tabix /tmp/k0XTRZeBY6/index.vcf.gz##idx##/tmp/k0XTRZeBY6/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /<>/test/test_view /tmp/k0XTRZeBY6/index2.bam 1:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/k0XTRZeBY6/index2.bam 1:2000000-2000000 .. ok test_index: /<>/test/test_view /tmp/k0XTRZeBY6/index2.bam 2:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/k0XTRZeBY6/index2.bam 2:2000000-2000000 .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/k0XTRZeBY6/index.bam.csi /<>/test/index.sam > /tmp/k0XTRZeBY6/index.bam .. ok test_index: /<>/test/test_index -c /tmp/k0XTRZeBY6/index.bam .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 0 -x /tmp/k0XTRZeBY6/index.bam.bai /<>/test/index.sam > /tmp/k0XTRZeBY6/index.bam .. ok test_index: /<>/test/test_index -b /tmp/k0XTRZeBY6/index.bam .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/k0XTRZeBY6/index.sam.gz.csi /<>/test/index.sam > /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/k0XTRZeBY6/index.sam.gz.bai /<>/test/index.sam > /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/k0XTRZeBY6/index.sam.gz.csi /<>/test/index_dos.sam > /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/k0XTRZeBY6/index.sam.gz.bai /<>/test/index_dos.sam > /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/k0XTRZeBY6/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -C -x /tmp/k0XTRZeBY6/index.cram.crai /<>/test/index.sam > /tmp/k0XTRZeBY6/index.cram .. ok test_index: /<>/test/test_index /tmp/k0XTRZeBY6/index.cram .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/k0XTRZeBY6/index.bcf.csi /<>/test/index.vcf > /tmp/k0XTRZeBY6/index.bcf .. ok test_index: /<>/test/test_index -c /tmp/k0XTRZeBY6/index.bcf .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/k0XTRZeBY6/index.vcf.gz.csi /<>/test/index.vcf > /tmp/k0XTRZeBY6/index.vcf.gz .. ok test_index: /<>/test/test_index -c /tmp/k0XTRZeBY6/index.vcf.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/k0XTRZeBY6/index.vcf.gz.tbi /<>/test/index.vcf > /tmp/k0XTRZeBY6/index.vcf.gz .. ok test_index: /<>/test/test_index -t /tmp/k0XTRZeBY6/index.vcf.gz .. ok test_index: /<>/tabix /tmp/k0XTRZeBY6/index.vcf.gz##idx##/tmp/k0XTRZeBY6/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /<>/test/test_view /tmp/k0XTRZeBY6/index2.bam 1:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/k0XTRZeBY6/index2.bam 1:2000000-2000000 .. ok test_index: /<>/test/test_view /tmp/k0XTRZeBY6/index2.bam 2:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/k0XTRZeBY6/index2.bam 2:2000000-2000000 .. ok test_view testing multi-ref CRAM modes: ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing multi-ref CRAM modes: ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=-1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=0 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ ./test_view -@4 -o seqs_per_slice=100 -o no_ref=1 -o multi_seq_per_slice=1 -S -C multi_ref.tmp.sam > multi_ref.tmp.cram ./test_view -@4 multi_ref.tmp.cram > multi_ref.tmp.sam_ ./compare_sam.pl multi_ref.tmp.sam multi_ref.tmp.sam_ .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing embed_ref=2: ./test_view -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out .. ok test_view testing BAM files with absent @SQ lines: ./test_view -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /<>/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_view testing auxf#values.sam, ref auxf.fa: ./test_view -@4 -S -l0 -b auxf#values.sam > auxf#values.tmp.bam ./test_view -@4 auxf#values.tmp.bam > auxf#values.tmp.bam.sam_ ./compare_sam.pl auxf#values.sam auxf#values.tmp.bam.sam_ ./test_view -@4 -t auxf.fa -S -C -o VERSION=2.1 auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -C -o VERSION=3.0 auxf#values.tmp.bam > auxf#values.tmp.bam.cram ./test_view -@4 auxf#values.tmp.bam.cram > auxf#values.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.bam.cram.bam.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=3.1 -o archive auxf#values.sam > auxf#values.tmp.cram ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -t auxf.fa -S -l7 -C -o VERSION=4.0 -o archive auxf#values.sam > auxf#values.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D auxf#values.tmp.cram > auxf#values.tmp.cram.sam_ ./compare_sam.pl -nomd auxf#values.sam auxf#values.tmp.cram.sam_ ./test_view -@4 -i reference=auxf.fa auxf#values_java.cram > auxf#values_java.tmp.sam_ ./compare_sam.pl -Baux -nomd auxf#values.sam auxf#values_java.tmp.sam_ .. ok test_view testing c1#bounds.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#bounds.sam > c1#bounds.tmp.bam ./test_view -@4 c1#bounds.tmp.bam > c1#bounds.tmp.bam.sam_ ./compare_sam.pl c1#bounds.sam c1#bounds.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#bounds.sam > c1#bounds.tmp.cram ./test_view -@4 -D c1#bounds.tmp.cram > c1#bounds.tmp.cram.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#bounds.tmp.bam > c1#bounds.tmp.bam.cram ./test_view -@4 c1#bounds.tmp.bam.cram > c1#bounds.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#bounds.sam c1#bounds.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#clip.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#clip.sam > c1#clip.tmp.bam ./test_view -@4 c1#clip.tmp.bam > c1#clip.tmp.bam.sam_ ./compare_sam.pl c1#clip.sam c1#clip.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#clip.sam > c1#clip.tmp.cram ./test_view -@4 -D c1#clip.tmp.cram > c1#clip.tmp.cram.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#clip.tmp.bam > c1#clip.tmp.bam.cram ./test_view -@4 c1#clip.tmp.bam.cram > c1#clip.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#clip.sam c1#clip.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#noseq.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#noseq.sam > c1#noseq.tmp.bam ./test_view -@4 c1#noseq.tmp.bam > c1#noseq.tmp.bam.sam_ ./compare_sam.pl c1#noseq.sam c1#noseq.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#noseq.sam > c1#noseq.tmp.cram ./test_view -@4 -D c1#noseq.tmp.cram > c1#noseq.tmp.cram.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#noseq.tmp.bam > c1#noseq.tmp.bam.cram ./test_view -@4 c1#noseq.tmp.bam.cram > c1#noseq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#noseq.sam c1#noseq.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad1.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad1.sam > c1#pad1.tmp.bam ./test_view -@4 c1#pad1.tmp.bam > c1#pad1.tmp.bam.sam_ ./compare_sam.pl c1#pad1.sam c1#pad1.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad1.sam > c1#pad1.tmp.cram ./test_view -@4 -D c1#pad1.tmp.cram > c1#pad1.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad1.tmp.bam > c1#pad1.tmp.bam.cram ./test_view -@4 c1#pad1.tmp.bam.cram > c1#pad1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad1.sam c1#pad1.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad2.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad2.sam > c1#pad2.tmp.bam ./test_view -@4 c1#pad2.tmp.bam > c1#pad2.tmp.bam.sam_ ./compare_sam.pl c1#pad2.sam c1#pad2.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad2.sam > c1#pad2.tmp.cram ./test_view -@4 -D c1#pad2.tmp.cram > c1#pad2.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad2.tmp.bam > c1#pad2.tmp.bam.cram ./test_view -@4 c1#pad2.tmp.bam.cram > c1#pad2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad2.sam c1#pad2.tmp.bam.cram.bam.sam_ .. ok test_view testing c1#pad3.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#pad3.sam > c1#pad3.tmp.bam ./test_view -@4 c1#pad3.tmp.bam > c1#pad3.tmp.bam.sam_ ./compare_sam.pl c1#pad3.sam c1#pad3.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#pad3.tmp.bam > c1#pad3.tmp.bam.cram ./test_view -@4 c1#pad3.tmp.bam.cram > c1#pad3.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.bam.cram.bam.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=3.1 -o archive c1#pad3.sam > c1#pad3.tmp.cram ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ ./test_view -@4 -t c1.fa -S -l7 -C -o VERSION=4.0 -o archive c1#pad3.sam > c1#pad3.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D c1#pad3.tmp.cram > c1#pad3.tmp.cram.sam_ ./compare_sam.pl -nomd c1#pad3.sam c1#pad3.tmp.cram.sam_ .. ok test_view testing c1#unknown.sam, ref c1.fa: ./test_view -@4 -S -l0 -b c1#unknown.sam > c1#unknown.tmp.bam ./test_view -@4 c1#unknown.tmp.bam > c1#unknown.tmp.bam.sam_ ./compare_sam.pl c1#unknown.sam c1#unknown.tmp.bam.sam_ ./test_view -@4 -t c1.fa -S -C -o VERSION=2.1 c1#unknown.sam > c1#unknown.tmp.cram ./test_view -@4 -D c1#unknown.tmp.cram > c1#unknown.tmp.cram.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.cram.sam_ ./test_view -@4 -t c1.fa -C -o VERSION=3.0 c1#unknown.tmp.bam > c1#unknown.tmp.bam.cram ./test_view -@4 c1#unknown.tmp.bam.cram > c1#unknown.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c1#unknown.sam c1#unknown.tmp.bam.cram.bam.sam_ .. ok test_view testing c2#pad.sam, ref c2.fa: ./test_view -@4 -S -l0 -b c2#pad.sam > c2#pad.tmp.bam ./test_view -@4 c2#pad.tmp.bam > c2#pad.tmp.bam.sam_ ./compare_sam.pl c2#pad.sam c2#pad.tmp.bam.sam_ ./test_view -@4 -t c2.fa -S -C -o VERSION=2.1 c2#pad.sam > c2#pad.tmp.cram ./test_view -@4 -D c2#pad.tmp.cram > c2#pad.tmp.cram.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.cram.sam_ ./test_view -@4 -t c2.fa -C -o VERSION=3.0 c2#pad.tmp.bam > c2#pad.tmp.bam.cram ./test_view -@4 c2#pad.tmp.bam.cram > c2#pad.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd c2#pad.sam c2#pad.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1.sam > ce#1.tmp.bam ./test_view -@4 ce#1.tmp.bam > ce#1.tmp.bam.sam_ ./compare_sam.pl ce#1.sam ce#1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1.sam > ce#1.tmp.cram ./test_view -@4 -D ce#1.tmp.cram > ce#1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1.tmp.bam > ce#1.tmp.bam.cram ./test_view -@4 ce#1.tmp.bam.cram > ce#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1.sam ce#1.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#1000.sam, ref ce.fa: ./test_view -@4 -S -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -S -l0 -b ce#1000.sam > ce#1000.tmp.bam ./test_view -@4 ce#1000.tmp.bam > ce#1000.tmp.bam.sam_ ./compare_sam.pl ce#1000.sam ce#1000.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l0 -C -o VERSION=3.0 ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000.tmp.bam > ce#1000.tmp.bam.cram ./test_view -@4 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#1000.tmp.bam.cram > ce#1000.tmp.bam.cram.ms ./test_view -@4 ce#1000.tmp.bam.cram.ms > ce#1000.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o fast ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o normal ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o small ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#1000.sam > ce#1000.tmp.cram ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#1000.sam > ce#1000.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#1000.tmp.cram > ce#1000.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000.sam ce#1000.tmp.cram.sam_ .. ok test_view testing ce#1000_er.tmp.cram.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.bam ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.sam_ ./compare_sam.pl ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#1000_er.tmp.cram.sam > ce#1000_er.tmp.cram.tmp.cram ./test_view -@4 -D ce#1000_er.tmp.cram.tmp.cram > ce#1000_er.tmp.cram.tmp.cram.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#1000_er.tmp.cram.tmp.bam > ce#1000_er.tmp.cram.tmp.bam.cram ./test_view -@4 ce#1000_er.tmp.cram.tmp.bam.cram > ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#2.sam > ce#2.tmp.bam ./test_view -@4 ce#2.tmp.bam > ce#2.tmp.bam.sam_ ./compare_sam.pl ce#2.sam ce#2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#2.sam > ce#2.tmp.cram ./test_view -@4 -D ce#2.tmp.cram > ce#2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#2.tmp.bam > ce#2.tmp.bam.cram ./test_view -@4 ce#2.tmp.bam.cram > ce#2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#2.sam ce#2.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#5.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5.sam > ce#5.tmp.bam ./test_view -@4 ce#5.tmp.bam > ce#5.tmp.bam.sam_ ./compare_sam.pl ce#5.sam ce#5.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5.tmp.bam > ce#5.tmp.bam.cram ./test_view -@4 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5.tmp.bam.cram > ce#5.tmp.bam.cram.ms ./test_view -@4 ce#5.tmp.bam.cram.ms > ce#5.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.bam.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#5.sam > ce#5.tmp.cram ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#5.sam > ce#5.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#5.tmp.cram > ce#5.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5.sam ce#5.tmp.cram.sam_ .. ok test_view testing ce#5b.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#5b.sam > ce#5b.tmp.bam ./test_view -@4 ce#5b.tmp.bam > ce#5b.tmp.bam.sam_ ./compare_sam.pl ce#5b.sam ce#5b.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#5b.sam > ce#5b.tmp.cram ./test_view -@4 -D ce#5b.tmp.cram > ce#5b.tmp.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#5b.tmp.bam > ce#5b.tmp.bam.cram ./test_view -@4 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#5b.tmp.bam.cram > ce#5b.tmp.bam.cram.ms ./test_view -@4 ce#5b.tmp.bam.cram.ms > ce#5b.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#5b.sam ce#5b.tmp.bam.cram.sam_ ./test_view -@4 -i reference=ce.fa ce#5b_java.cram > ce#5b_java.tmp.sam_ ./compare_sam.pl -Baux -nomd ce#5b.sam ce#5b_java.tmp.sam_ .. ok test_view testing ce#large_seq.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#large_seq.sam > ce#large_seq.tmp.bam ./test_view -@4 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.sam_ ./compare_sam.pl ce#large_seq.sam ce#large_seq.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#large_seq.tmp.bam > ce#large_seq.tmp.bam.cram ./test_view -@4 ce#large_seq.tmp.bam.cram > ce#large_seq.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o fast ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o normal ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o small ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#large_seq.sam > ce#large_seq.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#large_seq.tmp.cram > ce#large_seq.tmp.cram.sam_ ./compare_sam.pl -nomd ce#large_seq.sam ce#large_seq.tmp.cram.sam_ .. ok test_view testing ce#supp.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#supp.sam > ce#supp.tmp.bam ./test_view -@4 ce#supp.tmp.bam > ce#supp.tmp.bam.sam_ ./compare_sam.pl ce#supp.sam ce#supp.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#supp.tmp.bam > ce#supp.tmp.bam.cram ./test_view -@4 ce#supp.tmp.bam.cram > ce#supp.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=3.1 -o archive ce#supp.sam > ce#supp.tmp.cram ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ ./test_view -@4 -t ce.fa -S -l7 -C -o VERSION=4.0 -o archive ce#supp.sam > ce#supp.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D ce#supp.tmp.cram > ce#supp.tmp.cram.sam_ ./compare_sam.pl -nomd ce#supp.sam ce#supp.tmp.cram.sam_ .. ok test_view testing ce#tag_depadded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_depadded.sam > ce#tag_depadded.tmp.bam ./test_view -@4 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.sam_ ./compare_sam.pl ce#tag_depadded.sam ce#tag_depadded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_depadded.sam > ce#tag_depadded.tmp.cram ./test_view -@4 -D ce#tag_depadded.tmp.cram > ce#tag_depadded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_depadded.tmp.bam > ce#tag_depadded.tmp.bam.cram ./test_view -@4 ce#tag_depadded.tmp.bam.cram > ce#tag_depadded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_depadded.sam ce#tag_depadded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#tag_padded.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#tag_padded.sam > ce#tag_padded.tmp.bam ./test_view -@4 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.sam_ ./compare_sam.pl ce#tag_padded.sam ce#tag_padded.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#tag_padded.sam > ce#tag_padded.tmp.cram ./test_view -@4 -D ce#tag_padded.tmp.cram > ce#tag_padded.tmp.cram.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#tag_padded.tmp.bam > ce#tag_padded.tmp.bam.cram ./test_view -@4 ce#tag_padded.tmp.bam.cram > ce#tag_padded.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#tag_padded.sam ce#tag_padded.tmp.bam.cram.bam.sam_ .. ok test_view testing ce#unmap.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap.sam > ce#unmap.tmp.bam ./test_view -@4 ce#unmap.tmp.bam > ce#unmap.tmp.bam.sam_ ./compare_sam.pl ce#unmap.sam ce#unmap.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap.sam > ce#unmap.tmp.cram ./test_view -@4 -D ce#unmap.tmp.cram > ce#unmap.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap.tmp.bam > ce#unmap.tmp.bam.cram ./test_view -@4 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap.tmp.bam.cram > ce#unmap.tmp.bam.cram.ms ./test_view -@4 ce#unmap.tmp.bam.cram.ms > ce#unmap.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap.sam ce#unmap.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap1.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap1.sam > ce#unmap1.tmp.bam ./test_view -@4 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.sam_ ./compare_sam.pl ce#unmap1.sam ce#unmap1.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap1.sam > ce#unmap1.tmp.cram ./test_view -@4 -D ce#unmap1.tmp.cram > ce#unmap1.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap1.tmp.bam > ce#unmap1.tmp.bam.cram ./test_view -@4 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap1.tmp.bam.cram > ce#unmap1.tmp.bam.cram.ms ./test_view -@4 ce#unmap1.tmp.bam.cram.ms > ce#unmap1.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap1.sam ce#unmap1.tmp.bam.cram.sam_ .. ok test_view testing ce#unmap2.sam, ref ce.fa: ./test_view -@4 -S -l0 -b ce#unmap2.sam > ce#unmap2.tmp.bam ./test_view -@4 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.sam_ ./compare_sam.pl ce#unmap2.sam ce#unmap2.tmp.bam.sam_ ./test_view -@4 -t ce.fa -S -C -o VERSION=2.1 ce#unmap2.sam > ce#unmap2.tmp.cram ./test_view -@4 -D ce#unmap2.tmp.cram > ce#unmap2.tmp.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.cram.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 ce#unmap2.tmp.bam > ce#unmap2.tmp.bam.cram ./test_view -@4 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t ce.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 ce#unmap2.tmp.bam.cram > ce#unmap2.tmp.bam.cram.ms ./test_view -@4 ce#unmap2.tmp.bam.cram.ms > ce#unmap2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd ce#unmap2.sam ce#unmap2.tmp.bam.cram.sam_ .. ok test_view testing md#1.sam, ref md.fa: ./test_view -@4 -S -l0 -b md#1.sam > md#1.tmp.bam ./test_view -@4 md#1.tmp.bam > md#1.tmp.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.sam_ ./test_view -@4 -t md.fa -S -C -o VERSION=2.1 md#1.sam > md#1.tmp.cram ./test_view -@4 -D md#1.tmp.cram > md#1.tmp.cram.sam_ ./compare_sam.pl md#1.sam md#1.tmp.cram.sam_ ./test_view -@4 -t md.fa -C -o VERSION=3.0 md#1.tmp.bam > md#1.tmp.bam.cram ./test_view -@4 md#1.tmp.bam.cram > md#1.tmp.bam.cram.bam.sam_ ./compare_sam.pl md#1.sam md#1.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#blank.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#blank.sam > xx#blank.tmp.bam ./test_view -@4 xx#blank.tmp.bam > xx#blank.tmp.bam.sam_ ./compare_sam.pl xx#blank.sam xx#blank.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#blank.tmp.bam > xx#blank.tmp.bam.cram ./test_view -@4 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#blank.tmp.bam.cram > xx#blank.tmp.bam.cram.ms ./test_view -@4 xx#blank.tmp.bam.cram.ms > xx#blank.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#blank.sam > xx#blank.tmp.cram ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#blank.sam > xx#blank.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#blank.tmp.cram > xx#blank.tmp.cram.sam_ ./compare_sam.pl -nomd xx#blank.sam xx#blank.tmp.cram.sam_ .. ok test_view testing xx#large_aux.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux.sam > xx#large_aux.tmp.bam ./test_view -@4 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.sam_ ./compare_sam.pl xx#large_aux.sam xx#large_aux.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux.tmp.bam > xx#large_aux.tmp.bam.cram ./test_view -@4 xx#large_aux.tmp.bam.cram > xx#large_aux.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o fast xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o normal xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o small xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#large_aux.sam > xx#large_aux.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#large_aux.tmp.cram > xx#large_aux.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux.sam xx#large_aux.tmp.cram.sam_ ./test_view -@4 -i reference=xx.fa xx#large_aux_java.cram > xx#large_aux_java.tmp.sam_ [W::sanitise_SQ_lines] Header @SQ length mismatch for ref xx, 30 vs 20 ./compare_sam.pl -Baux -nomd xx#large_aux.sam xx#large_aux_java.tmp.sam_ .. ok test_view testing xx#large_aux2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#large_aux2.sam > xx#large_aux2.tmp.bam ./test_view -@4 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.sam_ ./compare_sam.pl xx#large_aux2.sam xx#large_aux2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#large_aux2.sam > xx#large_aux2.tmp.cram ./test_view -@4 -D xx#large_aux2.tmp.cram > xx#large_aux2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#large_aux2.tmp.bam > xx#large_aux2.tmp.bam.cram ./test_view -@4 xx#large_aux2.tmp.bam.cram > xx#large_aux2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#large_aux2.sam xx#large_aux2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#MD.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD.sam > xx#MD.tmp.bam ./test_view -@4 xx#MD.tmp.bam > xx#MD.tmp.bam.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD.tmp.bam > xx#MD.tmp.bam.cram ./test_view -@4 xx#MD.tmp.bam.cram > xx#MD.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#MD.sam > xx#MD.tmp.cram ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#MD.sam > xx#MD.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_view testing xx#MD2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#MD2.sam > xx#MD2.tmp.bam ./test_view -@4 xx#MD2.tmp.bam > xx#MD2.tmp.bam.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#MD2.sam > xx#MD2.tmp.cram ./test_view -@4 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#MD2.tmp.bam > xx#MD2.tmp.bam.cram ./test_view -@4 xx#MD2.tmp.bam.cram > xx#MD2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#MD2.sam xx#MD2.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#minimal.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#minimal.sam > xx#minimal.tmp.bam ./test_view -@4 xx#minimal.tmp.bam > xx#minimal.tmp.bam.sam_ ./compare_sam.pl xx#minimal.sam xx#minimal.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#minimal.sam > xx#minimal.tmp.cram ./test_view -@4 -D xx#minimal.tmp.cram > xx#minimal.tmp.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#minimal.tmp.bam > xx#minimal.tmp.bam.cram ./test_view -@4 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#minimal.tmp.bam.cram > xx#minimal.tmp.bam.cram.ms ./test_view -@4 xx#minimal.tmp.bam.cram.ms > xx#minimal.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#minimal.sam xx#minimal.tmp.bam.cram.sam_ .. ok test_view testing xx#pair.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#pair.sam > xx#pair.tmp.bam ./test_view -@4 xx#pair.tmp.bam > xx#pair.tmp.bam.sam_ ./compare_sam.pl xx#pair.sam xx#pair.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#pair.tmp.bam > xx#pair.tmp.bam.cram ./test_view -@4 xx#pair.tmp.bam.cram > xx#pair.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#pair.sam > xx#pair.tmp.cram ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#pair.sam > xx#pair.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#pair.tmp.cram > xx#pair.tmp.cram.sam_ ./compare_sam.pl -nomd xx#pair.sam xx#pair.tmp.cram.sam_ .. ok test_view testing xx#repeated.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#repeated.sam > xx#repeated.tmp.bam ./test_view -@4 xx#repeated.tmp.bam > xx#repeated.tmp.bam.sam_ ./compare_sam.pl xx#repeated.sam xx#repeated.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#repeated.sam > xx#repeated.tmp.cram ./test_view -@4 -D xx#repeated.tmp.cram > xx#repeated.tmp.cram.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#repeated.tmp.bam > xx#repeated.tmp.bam.cram ./test_view -@4 xx#repeated.tmp.bam.cram > xx#repeated.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#repeated.sam xx#repeated.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#rg.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#rg.sam > xx#rg.tmp.bam ./test_view -@4 xx#rg.tmp.bam > xx#rg.tmp.bam.sam_ ./compare_sam.pl xx#rg.sam xx#rg.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#rg.sam > xx#rg.tmp.cram ./test_view -@4 -D xx#rg.tmp.cram > xx#rg.tmp.cram.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#rg.tmp.bam > xx#rg.tmp.bam.cram ./test_view -@4 xx#rg.tmp.bam.cram > xx#rg.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#rg.sam xx#rg.tmp.bam.cram.bam.sam_ .. ok test_view testing xx#tlen.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen.sam > xx#tlen.tmp.bam ./test_view -@4 xx#tlen.tmp.bam > xx#tlen.tmp.bam.sam_ ./compare_sam.pl xx#tlen.sam xx#tlen.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen.tmp.bam > xx#tlen.tmp.bam.cram ./test_view -@4 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen.tmp.bam.cram > xx#tlen.tmp.bam.cram.ms ./test_view -@4 xx#tlen.tmp.bam.cram.ms > xx#tlen.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.bam.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=3.1 -o archive xx#tlen.sam > xx#tlen.tmp.cram ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ ./test_view -@4 -t xx.fa -S -l7 -C -o VERSION=4.0 -o archive xx#tlen.sam > xx#tlen.tmp.cram [W::cram_set_voption] CRAM version 4.0 is still a draft and subject to change. This is a technology demonstration that should not be used for archival data. ./test_view -@4 -D xx#tlen.tmp.cram > xx#tlen.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen.sam xx#tlen.tmp.cram.sam_ .. ok test_view testing xx#tlen2.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#tlen2.sam > xx#tlen2.tmp.bam ./test_view -@4 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.sam_ ./compare_sam.pl xx#tlen2.sam xx#tlen2.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#tlen2.sam > xx#tlen2.tmp.cram ./test_view -@4 -D xx#tlen2.tmp.cram > xx#tlen2.tmp.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#tlen2.tmp.bam > xx#tlen2.tmp.bam.cram ./test_view -@4 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#tlen2.tmp.bam.cram > xx#tlen2.tmp.bam.cram.ms ./test_view -@4 xx#tlen2.tmp.bam.cram.ms > xx#tlen2.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#tlen2.sam xx#tlen2.tmp.bam.cram.sam_ .. ok test_view testing xx#triplet.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#triplet.sam > xx#triplet.tmp.bam ./test_view -@4 xx#triplet.tmp.bam > xx#triplet.tmp.bam.sam_ ./compare_sam.pl xx#triplet.sam xx#triplet.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#triplet.sam > xx#triplet.tmp.cram ./test_view -@4 -D xx#triplet.tmp.cram > xx#triplet.tmp.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#triplet.tmp.bam > xx#triplet.tmp.bam.cram ./test_view -@4 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.bam.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 xx#triplet.tmp.bam.cram > xx#triplet.tmp.bam.cram.ms ./test_view -@4 xx#triplet.tmp.bam.cram.ms > xx#triplet.tmp.bam.cram.sam_ ./compare_sam.pl -nomd xx#triplet.sam xx#triplet.tmp.bam.cram.sam_ .. ok test_view testing xx#unsorted.sam, ref xx.fa: ./test_view -@4 -S -l0 -b xx#unsorted.sam > xx#unsorted.tmp.bam ./test_view -@4 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.sam_ ./compare_sam.pl xx#unsorted.sam xx#unsorted.tmp.bam.sam_ ./test_view -@4 -t xx.fa -S -C -o VERSION=2.1 xx#unsorted.sam > xx#unsorted.tmp.cram ./test_view -@4 -D xx#unsorted.tmp.cram > xx#unsorted.tmp.cram.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.cram.sam_ ./test_view -@4 -t xx.fa -C -o VERSION=3.0 xx#unsorted.tmp.bam > xx#unsorted.tmp.bam.cram ./test_view -@4 xx#unsorted.tmp.bam.cram > xx#unsorted.tmp.bam.cram.bam.sam_ ./compare_sam.pl -nomd xx#unsorted.sam xx#unsorted.tmp.bam.cram.bam.sam_ .. ok test_view testing embed_ref=2: ./test_view -@4 -C -p ce#1000_er.tmp.cram ce#1000.sam [W::cram_get_ref] Failed to populate reference for id 0 [W::cram_write_SAM_hdr] No M5 tags present and could not find reference [W::cram_write_SAM_hdr] Enabling embed_ref=2 option [W::cram_write_SAM_hdr] NOTE: the CRAM file will be bigger than using an external reference ./test_view -@4 -p ce#1000_er.tmp.cram.sam ce#1000_er.tmp.cram ./compare_sam.pl ce#1000.sam ce#1000_er.tmp.cram.sam .. ok test_view testing region queries: ./test_view -@4 -i reference=ce.fa range.cram CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out ./test_view -@4 range.bam CHROMOSOME_II:2980-2980 CHROMOSOME_IV:1500-1500 CHROMOSOME_II:2980-2980 CHROMOSOME_I:1000-1100 > range.tmp ./compare_sam.pl range.tmp range.out .. ok test_view testing BAM files with absent @SQ lines: ./test_view -@4 -p no_hdr_sq_1.tmp.sam no_hdr_sq_1.bam ./compare_sam.pl no_hdr_sq_1.tmp.sam no_hdr_sq_1.expected.sam ./test_view -@4 -p no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.bam CHROMOSOME_I ./compare_sam.pl no_hdr_sq_1.chr1.tmp.sam no_hdr_sq_1.expected.sam .. ok test_view testing large (> 2Gbases) positions: ./test_view -@4 -z -p longrefs/longref.tmp.sam.gz -x longrefs/longref.tmp.sam.gz.csi.otf -m 14 longrefs/longref.sam ./test_view -@4 -p longrefs/longref.tmp.sam_ longrefs/longref.tmp.sam.gz ./compare_sam.pl longrefs/longref.sam longrefs/longref.tmp.sam_ test_view: /<>/test/test_index -c longrefs/longref.tmp.sam.gz .. ok ./test_view -@4 -p longrefs/longref_itr.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 ./compare_sam.pl longrefs/longref_itr.expected.sam longrefs/longref_itr.tmp.sam ./test_view -@4 -M -p longrefs/longref_multi.tmp.sam longrefs/longref.tmp.sam.gz CHROMOSOME_I:10000000000-10000000003 CHROMOSOME_I:10000000100-10000000110 ./compare_sam.pl longrefs/longref_multi.expected.sam longrefs/longref_multi.tmp.sam .. ok test_MD testing xx#MD.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl xx#MD.sam xx#MD.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=0 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD.sam xx#MD.tmp.cram.sam_ Checking for MD/NM in xx#MD.sam ./test_view -t xx.fa -C xx#MD.sam > xx#MD.tmp.cram ./test_view -i decode_md=1 -D xx#MD.tmp.cram > xx#MD.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD.sam xx#MD.tmp.cram.sam_ .. ok test_MD testing xx#MD2.sam, ref xx.fa: ./test_view -o store_nm=1 -o store_md=1 -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=0 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=2 xx#MD2.sam xx#MD2.tmp.cram.sam_ ./test_view -t xx.fa -C xx#MD2.sam > xx#MD2.tmp.cram ./test_view -i decode_md=1 -D xx#MD2.tmp.cram > xx#MD2.tmp.cram.sam_ ./compare_sam.pl -partialmd=1 xx#MD2.sam xx#MD2.tmp.cram.sam_ .. ok test_vcf_api: /<>/test/test-vcf-api /tmp/k0XTRZeBY6/test-vcf-api.bcf .. ok test_bcf2vcf: /<>/test/test_view /<>/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /<>/test/test-vcf-sweep /tmp/k0XTRZeBY6/test-vcf-api.bcf .. ok test_vcf_various: /<>/htsfile -ch /<>/test/test-vcf-hdr-in.vcf .. ok test_vcf_various: /<>/htsfile -c /<>/test/formatcols.vcf .. ok test_vcf_various: /<>/htsfile -c /<>/test/noroundtrip.vcf .. ok test_vcf_various: /<>/htsfile -c /<>/test/formatmissing.vcf .. ok test_vcf_various: /<>/htsfile -c /<>/test/vcf_meta_meta.vcf .. ok test_vcf_various: /<>/test/test_view /<>/test/modhdr.vcf.gz chr22:1-2 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/k0XTRZeBY6 -s 74452500 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/k0XTRZeBY6 -s 34270147 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/k0XTRZeBY6 -s 11108528 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/k0XTRZeBY6 -s 42233895 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/k0XTRZeBY6 -s 8111117 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/k0XTRZeBY6 -s 85644070 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/k0XTRZeBY6 -s 49879942 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/k0XTRZeBY6 -s 47881429 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/k0XTRZeBY6 -s 69081244 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/k0XTRZeBY6 -s 83459376 .. ok test_bcf_sr_no_index: /<>/test/test-bcf-sr --no-index -p all --args /<>/test/bcf-sr/merge.noidx.a.vcf /<>/test/bcf-sr/merge.noidx.b.vcf /<>/test/bcf-sr/merge.noidx.c.vcf 2> /tmp/k0XTRZeBY6/no_index_1.err .. ok test_bcf_sr_no_index: /<>/test/test-bcf-sr --no-index -p all --args /<>/test/bcf-sr/merge.noidx.a.vcf /<>/test/bcf-sr/merge.noidx.hdr_order.vcf > /tmp/k0XTRZeBY6/no_index_2.out 2> /tmp/k0XTRZeBY6/no_index_2.err (expected fail) .. ok test_bcf_sr_no_index: /<>/test/test-bcf-sr --no-index -p all --args /<>/test/bcf-sr/merge.noidx.a.vcf /<>/test/bcf-sr/merge.noidx.rec_order.vcf > /tmp/k0XTRZeBY6/no_index_3.out 2> /tmp/k0XTRZeBY6/no_index_3.err (expected fail) .. ok test_bcf_sr_no_index: /<>/test/test-bcf-sr --no-index -p all --args /<>/test/bcf-sr/merge.noidx.rec_order.vcf /<>/test/bcf-sr/merge.noidx.a.vcf > /tmp/k0XTRZeBY6/no_index_4.out 2> /tmp/k0XTRZeBY6/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /<>/test/test_view -b -p /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf -x /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf.csi /<>/test/bcf-sr/weird-chr-names.vcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_1.out.vcf -r '1' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_2.out.vcf -r '1:1-2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_4.out.vcf -r '1:1-1' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_5.out.vcf -r '{1:1}' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set regions .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_14.out.vcf -t '1' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_15.out.vcf -t '1:1-2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_17.out.vcf -t '1:1-1' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_18.out.vcf -t '{1:1}' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/k0XTRZeBY6/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/k0XTRZeBY6/weird-chr-names.vcf.bcf (expected fail) [E::_regions_init_string] Could not parse the region(s): {1:1-1}-2 Failed to set targets .. ok test_command: /<>/test/test-bcf-translate - .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/k0XTRZeBY6/headernul0.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/k0XTRZeBY6/headernul1.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/k0XTRZeBY6/headernul678.bam .. ok test_rebgzip: Alternate zlib/deflate library detected test_rebgzip: /<>/bgzip -I /<>/test/bgziptest.txt.tmp.gz.gzi -c -g /<>/test/bgziptest.txt .. ok test-logging: /<>/test/test-logging.pl .. ok test_plugin_loading: HTS_PATH=/<> /<>/test/with-shlib.sh /<>/htsfile https://localhost:99999/invalid_port .. ok test_realn: /<>/test/test_realn -f /<>/test/realn01.fa -i /<>/test/realn01.sam -o - .. ok test_realn: /<>/test/test_realn -f /<>/test/realn02.fa -i /<>/test/realn02.sam -o - .. ok test_realn: /<>/test/test_realn -a -f /<>/test/realn01.fa -i /<>/test/realn01.sam -o - .. ok test_realn: /<>/test/test_realn -a -f /<>/test/realn02.fa -i /<>/test/realn02.sam -o - .. ok test_realn: /<>/test/test_realn -e -f /<>/test/realn01.fa -i /<>/test/realn01.sam -o - .. ok test_realn: /<>/test/test_realn -e -f /<>/test/realn02.fa -i /<>/test/realn02.sam -o - .. ok test_realn: /<>/test/test_realn -r -f /<>/test/realn02.fa -i /<>/test/realn02-r.sam -o - .. ok test_realn: /<>/test/test_realn -a -f /<>/test/realn02.fa -i /<>/test/realn02_exp.sam -o - .. ok test_realn: /<>/test/test_realn -f /<>/test/realn02.fa -i /<>/test/realn02_exp-a.sam -o - .. ok test_realn: /<>/test/test_realn -f /<>/test/realn03.fa -e -i /<>/test/realn03.sam -o - .. ok test-bcf_set_variant_type: /<>/test/test-bcf_set_variant_type .. ok run_annot_tsv: /<>/annot-tsv -f smpl:overlap --allow-dups -s /<>/test/annot-tsv/src.1.txt -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.1.txt | /<>/annot-tsv -f smpl:overlap --allow-dups -s /<>/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.1.txt | /<>/annot-tsv -f smpl:overlap --allow-dups -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /<>/annot-tsv -f smpl:overlap -s /<>/test/annot-tsv/src.1.txt -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.1.txt | /<>/annot-tsv -f smpl:overlap -s /<>/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.1.txt | /<>/annot-tsv -f smpl:overlap -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /<>/annot-tsv -f smpl:overlap -c chr,beg,end -s /<>/test/annot-tsv/src.1.txt -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.1.txt | /<>/annot-tsv -f smpl:overlap -c chr,beg,end -s /<>/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.1.txt | /<>/annot-tsv -f smpl:overlap -c chr,beg,end -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /<>/annot-tsv -f smpl,value:overlap,value -s /<>/test/annot-tsv/src.1.txt -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.1.txt | /<>/annot-tsv -f smpl,value:overlap,value -s /<>/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.1.txt | /<>/annot-tsv -f smpl,value:overlap,value -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /<>/annot-tsv -f smpl:overlap -O 0.5 -s /<>/test/annot-tsv/src.1.txt -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.1.txt | /<>/annot-tsv -f smpl:overlap -O 0.5 -s /<>/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.1.txt | /<>/annot-tsv -f smpl:overlap -O 0.5 -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /<>/annot-tsv -f smpl:overlap -rO 0.5 -s /<>/test/annot-tsv/src.1.txt -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.1.txt | /<>/annot-tsv -f smpl:overlap -rO 0.5 -s /<>/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.1.txt | /<>/annot-tsv -f smpl:overlap -rO 0.5 -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /<>/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /<>/test/annot-tsv/src.1.txt -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.1.txt | /<>/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -s /<>/test/annot-tsv/src.1.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.1.txt | /<>/annot-tsv -f smpl:overlap --allow-dups --max-annots 2 -t /<>/test/annot-tsv/dst.1.txt .. ok run_annot_tsv: /<>/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /<>/test/annot-tsv/src.2.txt -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -s /<>/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /<>/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /<>/test/annot-tsv/src.2.txt -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -s /<>/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f 4:5 -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /<>/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /<>/test/annot-tsv/src.2.txt -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -s /<>/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f 4,value:5,value -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /<>/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /<>/test/annot-tsv/src.2.txt -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -s /<>/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /<>/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /<>/test/annot-tsv/src.2.txt -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -s /<>/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f value,4:value,5 -a nbp,frac -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /<>/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /<>/test/annot-tsv/src.2.txt -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -s /<>/test/annot-tsv/src.2.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.2.txt | /<>/annot-tsv -c 1,2,3:1,2,3 -f 4:5 --allow-dups --max-annots 2 -t /<>/test/annot-tsv/dst.2.txt .. ok run_annot_tsv: /<>/annot-tsv -f smpl:overlap -a nbp,frac -s /<>/test/annot-tsv/src.3.txt -t /<>/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.3.txt | /<>/annot-tsv -f smpl:overlap -a nbp,frac -s /<>/test/annot-tsv/src.3.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.3.txt | /<>/annot-tsv -f smpl:overlap -a nbp,frac -t /<>/test/annot-tsv/dst.3.txt .. ok run_annot_tsv: /<>/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /<>/test/annot-tsv/src.4.txt -t /<>/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.4.txt | /<>/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -s /<>/test/annot-tsv/src.4.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.4.txt | /<>/annot-tsv -c 2,3,4:2,3,4 -m 1:1 -f 1:1 -a nbp,frac -t /<>/test/annot-tsv/dst.4.txt .. ok run_annot_tsv: /<>/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /<>/test/annot-tsv/src.5.txt -t /<>/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.5.txt | /<>/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -s /<>/test/annot-tsv/src.5.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.5.txt | /<>/annot-tsv -c 2,3,4:2,3,4 -a nbp,frac -t /<>/test/annot-tsv/dst.5.txt .. ok run_annot_tsv: /<>/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /<>/test/annot-tsv/src.6.txt -t /<>/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.6.txt | /<>/annot-tsv -c 1,2,2:1,2,2 -a nbp -s /<>/test/annot-tsv/src.6.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.6.txt | /<>/annot-tsv -c 1,2,2:1,2,2 -a nbp -t /<>/test/annot-tsv/dst.6.txt .. ok run_annot_tsv: /<>/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /<>/test/annot-tsv/src.7.txt -t /<>/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.7.txt | /<>/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -s /<>/test/annot-tsv/src.7.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.7.txt | /<>/annot-tsv -c 1,2,2:1,2,2 -f overlap -H -t /<>/test/annot-tsv/dst.7.txt .. ok run_annot_tsv: /<>/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /<>/test/annot-tsv/src.8.txt -t /<>/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.8.txt | /<>/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -s /<>/test/annot-tsv/src.8.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.8.txt | /<>/annot-tsv -c chr,beg,end:chr,start,end -m sample -f is_tp -t /<>/test/annot-tsv/dst.8.txt .. ok run_annot_tsv: /<>/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /<>/test/annot-tsv/src.9.txt -t /<>/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.9.txt | /<>/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -s /<>/test/annot-tsv/src.9.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.9.txt | /<>/annot-tsv -c 1,2,3:chr,beg,end -a nbp,frac,cnt -t /<>/test/annot-tsv/dst.9.txt .. ok run_annot_tsv: /<>/annot-tsv -f smpl -s /<>/test/annot-tsv/src.10.txt -t /<>/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.10.txt | /<>/annot-tsv -f smpl -s /<>/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.10.txt | /<>/annot-tsv -f smpl -t /<>/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /<>/annot-tsv -s /<>/test/annot-tsv/src.10.txt -t /<>/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.10.txt | /<>/annot-tsv -s /<>/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.10.txt | /<>/annot-tsv -t /<>/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /<>/annot-tsv -x -s /<>/test/annot-tsv/src.10.txt -t /<>/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.10.txt | /<>/annot-tsv -x -s /<>/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.10.txt | /<>/annot-tsv -x -t /<>/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /<>/annot-tsv -m smpl -f smpl -s /<>/test/annot-tsv/src.10.txt -t /<>/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.10.txt | /<>/annot-tsv -m smpl -f smpl -s /<>/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.10.txt | /<>/annot-tsv -m smpl -f smpl -t /<>/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /<>/annot-tsv -m smpl -s /<>/test/annot-tsv/src.10.txt -t /<>/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.10.txt | /<>/annot-tsv -m smpl -s /<>/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.10.txt | /<>/annot-tsv -m smpl -t /<>/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: /<>/annot-tsv -m smpl -x -s /<>/test/annot-tsv/src.10.txt -t /<>/test/annot-tsv/dst.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/dst.10.txt | /<>/annot-tsv -m smpl -x -s /<>/test/annot-tsv/src.10.txt .. ok run_annot_tsv: cat /<>/test/annot-tsv/src.10.txt | /<>/annot-tsv -m smpl -x -t /<>/test/annot-tsv/dst.10.txt .. ok Number of tests: total .. 291 passed .. 291 failed .. 0 make[2]: Leaving directory '/<>' rm -fr -- /tmp/dh-xdg-rundir-nKV7pHXG make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a rm -f -- debian/libhts3t64.substvars debian/libhts-dev.substvars debian/tabix.substvars rm -fr -- debian/.debhelper/generated/libhts3t64/ debian/libhts3t64/ debian/tmp/ debian/.debhelper/generated/libhts-dev/ debian/libhts-dev/ debian/.debhelper/generated/tabix/ debian/tabix/ rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_auto_install-arch make[1]: Entering directory '/<>' for binary in sam test-regidx hts_endian test-bcf-sr test_bgzf ; do \ rm /<>/test/${binary} ; \ done dh_auto_install -- prefix=/usr \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="-I. -DSAMTOOLS=1 $(dpkg-buildflags --get CPPFLAGS)" \ PACKAGE_VERSION="1.19" \ libdir=/usr/lib/arm-linux-gnueabihf install -m0755 -d /<>/htslib-1.19\+ds/debian/tmp make -j4 install DESTDIR=/<>/htslib-1.19\+ds/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/htslib-1.19+ds-1.1build3 -ffat-lto-objects -ffat-lto-objects" "CPPFLAGS=-I. -DSAMTOOLS=1 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3" PACKAGE_VERSION=1.19 libdir=/usr/lib/arm-linux-gnueabihf make[2]: Entering directory '/<>' mkdir -p -m 755 /<>/debian/tmp/usr/bin /<>/debian/tmp/usr/include /<>/debian/tmp/usr/include/htslib /<>/debian/tmp/usr/lib/arm-linux-gnueabihf /<>/debian/tmp/usr/share/man/man1 /<>/debian/tmp/usr/share/man/man5 /<>/debian/tmp/usr/share/man/man7 /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig if test -n "/usr/lib/arm-linux-gnueabihf/htslib"; then mkdir -p -m 755 /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/htslib; fi install -p -m 644 libhts.so /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/arm-linux-gnueabihf#g;s#@-PACKAGE_VERSION@#1.19#g' htslib.pc.tmp > /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc ln -sf libhts.so.1.19 /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so chmod 644 /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc ln -sf libhts.so.1.19 /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3 install -p annot-tsv bgzip htsfile tabix /<>/debian/tmp/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/htslib; fi install -p -m 644 htslib/*.h /<>/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /<>/debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a install -p -m 644 annot-tsv.1 bgzip.1 htsfile.1 tabix.1 /<>/debian/tmp/usr/share/man/man1 install -p -m 644 faidx.5 sam.5 vcf.5 /<>/debian/tmp/usr/share/man/man5 install -p -m 644 htslib-s3-plugin.7 /<>/debian/tmp/usr/share/man/man7 make[2]: Leaving directory '/<>' # restore clean copy of test dir before dh_install is run # This should not be done earlier since dh_auto_install contains some unconditional removals rm -f -r test mv test_backup test make[1]: Leaving directory '/<>' dh_install -a install -m0755 -d debian/libhts3t64/usr/lib/arm-linux-gnueabihf cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/htslib debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so.3 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/ install -m0755 -d debian/libhts3t64/usr/share/man/man5 cp --reflink=auto -a debian/tmp/usr/share/man/man5/faidx.5 debian/tmp/usr/share/man/man5/sam.5 debian/tmp/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man5/ install -m0755 -d debian/libhts-dev/usr/include cp --reflink=auto -a debian/tmp/usr/include/htslib debian/libhts-dev/usr/include/ install -m0755 -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.a debian/tmp/usr/lib/arm-linux-gnueabihf/libhts.so debian/libhts-dev/usr/lib/arm-linux-gnueabihf/ install -m0755 -d debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/arm-linux-gnueabihf/pkgconfig/ install -m0755 -d debian/tabix/usr/bin cp --reflink=auto -a ./bgzip ./htsfile ./tabix debian/tabix/usr/bin/ rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_installdocs make[1]: Entering directory '/<>' dh_installdocs install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/copyright debian/libhts3t64/usr/share/doc/libhts3t64/copyright install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./debian/README.test debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README debian/libhts-dev/usr/share/doc/libhts-dev cp --reflink=auto -a ./README.large_positions.md debian/libhts-dev/usr/share/doc/libhts-dev chmod -R u\+rw,go=rX debian/libhts-dev/usr/share/doc install -p -m0644 debian/copyright debian/libhts-dev/usr/share/doc/libhts-dev/copyright install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/copyright debian/tabix/usr/share/doc/tabix/copyright # Fix Perl interpreter path for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so: No such file or directory make[1]: Leaving directory '/<>' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs NEWS install -m0755 -d debian/libhts3t64/usr/share/doc/libhts3t64 install -p -m0644 debian/.debhelper/generated/libhts3t64/dh_installchangelogs.dch.trimmed debian/libhts3t64/usr/share/doc/libhts3t64/changelog.Debian install -p -m0644 NEWS debian/libhts3t64/usr/share/doc/libhts3t64/changelog install -m0755 -d debian/libhts-dev/usr/share/doc/libhts-dev install -p -m0644 debian/.debhelper/generated/libhts-dev/dh_installchangelogs.dch.trimmed debian/libhts-dev/usr/share/doc/libhts-dev/changelog.Debian install -p -m0644 NEWS debian/libhts-dev/usr/share/doc/libhts-dev/changelog install -m0755 -d debian/tabix/usr/share/doc/tabix install -p -m0644 debian/.debhelper/generated/tabix/dh_installchangelogs.dch.trimmed debian/tabix/usr/share/doc/tabix/changelog.Debian install -p -m0644 NEWS debian/tabix/usr/share/doc/tabix/changelog make[1]: Leaving directory '/<>' dh_installman -a install -m0755 -d debian/libhts3t64/usr/share/man/man7/ install -p -m0644 ./htslib-s3-plugin.7 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./htsfile.1 debian/tabix/usr/share/man/man1/htsfile.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./tabix.1 debian/tabix/usr/share/man/man1/tabix.1 install -m0755 -d debian/tabix/usr/share/man/man1/ install -p -m0644 ./bgzip.1 debian/tabix/usr/share/man/man1/bgzip.1 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3t64/usr/share/man/man5/faidx.5 debian/libhts3t64/usr/share/man/man5/sam.5 man-recode --to-code UTF-8 --suffix .dh-new debian/libhts3t64/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1 man-recode --to-code UTF-8 --suffix .dh-new debian/tabix/usr/share/man/man1/tabix.1 mv debian/tabix/usr/share/man/man1/tabix.1.dh-new debian/tabix/usr/share/man/man1/tabix.1 chmod 0644 -- debian/tabix/usr/share/man/man1/tabix.1 mv debian/tabix/usr/share/man/man1/bgzip.1.dh-new debian/tabix/usr/share/man/man1/bgzip.1 mv debian/tabix/usr/share/man/man1/htsfile.1.dh-new debian/tabix/usr/share/man/man1/htsfile.1 chmod 0644 -- debian/tabix/usr/share/man/man1/bgzip.1 debian/tabix/usr/share/man/man1/htsfile.1 mv debian/libhts3t64/usr/share/man/man5/faidx.5.dh-new debian/libhts3t64/usr/share/man/man5/faidx.5 mv debian/libhts3t64/usr/share/man/man5/sam.5.dh-new debian/libhts3t64/usr/share/man/man5/sam.5 chmod 0644 -- debian/libhts3t64/usr/share/man/man5/faidx.5 debian/libhts3t64/usr/share/man/man5/sam.5 mv debian/libhts3t64/usr/share/man/man5/vcf.5.dh-new debian/libhts3t64/usr/share/man/man5/vcf.5 mv debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 chmod 0644 -- debian/libhts3t64/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 dh_lintian -a install -m0755 -d debian/libhts3t64/usr/share/lintian/overrides install -p -m0644 debian/libhts3t64.lintian-overrides debian/libhts3t64/usr/share/lintian/overrides/libhts3t64 dh_perl -a dh_link -a rm -f debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.3 ln -s libhts.so.1.19 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.3 rm -f debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so ln -s libhts.so.1.19 debian/libhts-dev/usr/lib/arm-linux-gnueabihf/libhts.so install -m0755 -d debian/tabix/usr/share/man/man1 rm -f debian/tabix/usr/share/man/man1/bgzip.1.gz ln -s tabix.1.gz debian/tabix/usr/share/man/man1/bgzip.1.gz dh_strip_nondeterminism -a dh_compress -a cd debian/libhts3t64 cd debian/libhts-dev cd debian/tabix chmod a-x usr/share/doc/libhts3t64/changelog usr/share/doc/libhts3t64/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 chmod a-x usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 chmod a-x usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian gzip -9nf usr/share/doc/libhts3t64/changelog usr/share/doc/libhts3t64/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 gzip -9nf usr/share/doc/tabix/changelog usr/share/doc/tabix/changelog.Debian usr/share/man/man1/bgzip.1 usr/share/man/man1/htsfile.1 usr/share/man/man1/tabix.1 gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian cd '/<>' cd '/<>' cd '/<>' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian/libhts3t64 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/tabix ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libhts3t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts3t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts3t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts3t64/usr/share/man debian/libhts3t64/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/tabix/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/libhts-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian -name simple_test_driver.sh -exec chmod +x \{\} \; make[1]: Leaving directory '/<>' rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_missing make[1]: Entering directory '/<>' # FIXME: No idea why these files are remaining in debian/tmp rm -rf debian/tmp/usr/bin debian/tmp/usr/share/man dh_missing make[1]: Leaving directory '/<>' dh_dwz -a install -m0755 -d debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf dwz -mdebian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix install -m0755 -d debian/libhts3t64/usr/lib/debug/.dwz/arm-linux-gnueabihf dwz -mdebian/libhts3t64/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3t64.debug -M/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3t64.debug -- debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 dwz: debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19: DWARF compression not beneficial - old size 847395 new size 867339 objcopy --compress-debug-sections debian/libhts3t64/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3t64.debug chmod 0644 -- debian/libhts3t64/usr/lib/debug/.dwz/arm-linux-gnueabihf/libhts3t64.debug objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug chmod 0644 -- debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf/tabix.debug rm -f debian/libhts-dev.debhelper.log debian/libhts3t64.debhelper.log debian/tabix.debhelper.log debian/rules override_dh_strip make[1]: Entering directory '/<>' # This is apparently important for the interpretation by ldc2 in sambamba dh_strip -Xlibhts.a debugedit --build-id --build-id-seed=tabix/1.19\+ds-1.1build3 debian/tabix/usr/bin/tabix debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 debugedit: debian/tabix/usr/bin/tabix: Unknown DWARF DW_FORM_0x1f20 2d50a101dac9cdaabce2521bef11dab2845a2cf7 install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2d objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2d/50a101dac9cdaabce2521bef11dab2845a2cf7.debug fd8dc793142324e15c6e76a383142e9c84259f07 install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/fd objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/fd/8dc793142324e15c6e76a383142e9c84259f07.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2d/50a101dac9cdaabce2521bef11dab2845a2cf7.debug strip --remove-section=.comment --remove-section=.note -o /tmp/cRrW7FB5_8/stripdcnM2T debian/tabix/usr/bin/tabix chmod --reference debian/tabix/usr/bin/tabix /tmp/cRrW7FB5_8/stripdcnM2T cat '/tmp/cRrW7FB5_8/stripdcnM2T' > 'debian/tabix/usr/bin/tabix' chmod --reference /tmp/cRrW7FB5_8/stripdcnM2T debian/tabix/usr/bin/tabix objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/2d/50a101dac9cdaabce2521bef11dab2845a2cf7.debug debian/tabix/usr/bin/tabix /tmp/cRrW7FB5_8/objcopyjlcMOv chmod --reference debian/tabix/usr/bin/tabix /tmp/cRrW7FB5_8/objcopyjlcMOv cat '/tmp/cRrW7FB5_8/objcopyjlcMOv' > 'debian/tabix/usr/bin/tabix' chmod --reference /tmp/cRrW7FB5_8/objcopyjlcMOv debian/tabix/usr/bin/tabix chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/fd/8dc793142324e15c6e76a383142e9c84259f07.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/9E66DxN73B/striphuC7ao debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 debugedit --build-id --build-id-seed=tabix/1.19\+ds-1.1build3 debian/tabix/usr/bin/htsfile chmod --reference debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 /tmp/9E66DxN73B/striphuC7ao debugedit: debian/tabix/usr/bin/htsfile: Unknown DWARF DW_FORM_0x1f20 cat '/tmp/9E66DxN73B/striphuC7ao' > 'debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19' chmod --reference /tmp/9E66DxN73B/striphuC7ao debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 817fb5c936fb578fa4a64569093b524c3cab6108 objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/fd/8dc793142324e15c6e76a383142e9c84259f07.debug debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 /tmp/9E66DxN73B/objcopyRsU2Oc install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/81 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/81/7fb5c936fb578fa4a64569093b524c3cab6108.debug chmod --reference debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 /tmp/9E66DxN73B/objcopyRsU2Oc cat '/tmp/9E66DxN73B/objcopyRsU2Oc' > 'debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19' chmod --reference /tmp/9E66DxN73B/objcopyRsU2Oc debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debugedit: debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so: Unknown DWARF DW_FORM_0x1f20 16af9f42d7cf3f1d0b3b76d8620c81b472766554 install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/16 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/16/af9f42d7cf3f1d0b3b76d8620c81b472766554.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/16/af9f42d7cf3f1d0b3b76d8620c81b472766554.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/9E66DxN73B/strip_xztZ4 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so chmod --reference debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so /tmp/9E66DxN73B/strip_xztZ4 cat '/tmp/9E66DxN73B/strip_xztZ4' > 'debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so' chmod --reference /tmp/9E66DxN73B/strip_xztZ4 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/16/af9f42d7cf3f1d0b3b76d8620c81b472766554.debug debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so /tmp/9E66DxN73B/objcopyN6QleU chmod --reference debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so /tmp/9E66DxN73B/objcopyN6QleU cat '/tmp/9E66DxN73B/objcopyN6QleU' > 'debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so' chmod --reference /tmp/9E66DxN73B/objcopyN6QleU debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debugedit: debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so: Unknown DWARF DW_FORM_0x1f21 04f9b674cb3cb5429bbbaddb3b185362f2d46e2f install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/04 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/04/f9b674cb3cb5429bbbaddb3b185362f2d46e2f.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/04/f9b674cb3cb5429bbbaddb3b185362f2d46e2f.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/9E66DxN73B/stripnKrzcS debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so chmod --reference debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so /tmp/9E66DxN73B/stripnKrzcS cat '/tmp/9E66DxN73B/stripnKrzcS' > 'debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so' chmod --reference /tmp/9E66DxN73B/stripnKrzcS debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/04/f9b674cb3cb5429bbbaddb3b185362f2d46e2f.debug debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so /tmp/9E66DxN73B/objcopyj_eEJN chmod --reference debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so /tmp/9E66DxN73B/objcopyj_eEJN cat '/tmp/9E66DxN73B/objcopyj_eEJN' > 'debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so' chmod --reference /tmp/9E66DxN73B/objcopyj_eEJN debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debugedit: debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so: Unknown DWARF DW_FORM_0x1f21 7e7e25078afea2fe9c2c00abd4cf9493ea64da5b install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7e objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7e/7e25078afea2fe9c2c00abd4cf9493ea64da5b.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7e/7e25078afea2fe9c2c00abd4cf9493ea64da5b.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/9E66DxN73B/stripaa9Hvu debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so chmod --reference debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so /tmp/9E66DxN73B/stripaa9Hvu cat '/tmp/9E66DxN73B/stripaa9Hvu' > 'debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so' chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/81/7fb5c936fb578fa4a64569093b524c3cab6108.debug strip --remove-section=.comment --remove-section=.note -o /tmp/cRrW7FB5_8/stripDZj1d0 debian/tabix/usr/bin/htsfile chmod --reference /tmp/9E66DxN73B/stripaa9Hvu debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so chmod --reference debian/tabix/usr/bin/htsfile /tmp/cRrW7FB5_8/stripDZj1d0 objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7e/7e25078afea2fe9c2c00abd4cf9493ea64da5b.debug debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so /tmp/9E66DxN73B/objcopy7afBjr cat '/tmp/cRrW7FB5_8/stripDZj1d0' > 'debian/tabix/usr/bin/htsfile' chmod --reference debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so /tmp/9E66DxN73B/objcopy7afBjr chmod --reference /tmp/cRrW7FB5_8/stripDZj1d0 debian/tabix/usr/bin/htsfile cat '/tmp/9E66DxN73B/objcopy7afBjr' > 'debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so' objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/81/7fb5c936fb578fa4a64569093b524c3cab6108.debug debian/tabix/usr/bin/htsfile /tmp/cRrW7FB5_8/objcopyASxTUV chmod --reference /tmp/9E66DxN73B/objcopy7afBjr debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so chmod --reference debian/tabix/usr/bin/htsfile /tmp/cRrW7FB5_8/objcopyASxTUV debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so cat '/tmp/cRrW7FB5_8/objcopyASxTUV' > 'debian/tabix/usr/bin/htsfile' debugedit: debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so: Unknown DWARF DW_FORM_0x1f21 000bf1efba4e77ba922732d940bb5924e4b32c39 chmod --reference /tmp/cRrW7FB5_8/objcopyASxTUV debian/tabix/usr/bin/htsfile install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/00 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/00/0bf1efba4e77ba922732d940bb5924e4b32c39.debug debugedit --build-id --build-id-seed=tabix/1.19\+ds-1.1build3 debian/tabix/usr/bin/bgzip debugedit: debian/tabix/usr/bin/bgzip: Unknown DWARF DW_FORM_0x1f20 chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/00/0bf1efba4e77ba922732d940bb5924e4b32c39.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/9E66DxN73B/stripdoiE3a debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so bec9d1b3f9c28047364d2fed696efd8e601eebd6 chmod --reference debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so /tmp/9E66DxN73B/stripdoiE3a cat '/tmp/9E66DxN73B/stripdoiE3a' > 'debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so' install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be/c9d1b3f9c28047364d2fed696efd8e601eebd6.debug chmod --reference /tmp/9E66DxN73B/stripdoiE3a debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/00/0bf1efba4e77ba922732d940bb5924e4b32c39.debug debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so /tmp/9E66DxN73B/objcopy03CFqt chmod --reference debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so /tmp/9E66DxN73B/objcopy03CFqt cat '/tmp/9E66DxN73B/objcopy03CFqt' > 'debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so' chmod --reference /tmp/9E66DxN73B/objcopy03CFqt debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/libhts3t64/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/libhts3t64/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/libhts3t64/usr/lib/debug install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc ln -s libhts3t64 debian/.debhelper/libhts3t64/dbgsym-root/usr/share/doc/libhts3t64-dbgsym install -m0755 -d debian/.debhelper/libhts3t64 chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be/c9d1b3f9c28047364d2fed696efd8e601eebd6.debug strip --remove-section=.comment --remove-section=.note -o /tmp/cRrW7FB5_8/stripf2ASu5 debian/tabix/usr/bin/bgzip chmod --reference debian/tabix/usr/bin/bgzip /tmp/cRrW7FB5_8/stripf2ASu5 cat '/tmp/cRrW7FB5_8/stripf2ASu5' > 'debian/tabix/usr/bin/bgzip' chmod --reference /tmp/cRrW7FB5_8/stripf2ASu5 debian/tabix/usr/bin/bgzip objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/be/c9d1b3f9c28047364d2fed696efd8e601eebd6.debug debian/tabix/usr/bin/bgzip /tmp/cRrW7FB5_8/objcopyQJ9Qvp chmod --reference debian/tabix/usr/bin/bgzip /tmp/cRrW7FB5_8/objcopyQJ9Qvp cat '/tmp/cRrW7FB5_8/objcopyQJ9Qvp' > 'debian/tabix/usr/bin/bgzip' chmod --reference /tmp/cRrW7FB5_8/objcopyQJ9Qvp debian/tabix/usr/bin/bgzip install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/arm-linux-gnueabihf debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/tabix/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/tabix/usr/lib/debug install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/share/doc ln -s tabix debian/.debhelper/tabix/dbgsym-root/usr/share/doc/tabix-dbgsym install -m0755 -d debian/.debhelper/tabix make[1]: Leaving directory '/<>' dh_makeshlibs -a rm -f debian/libhts3t64/DEBIAN/shlibs install -m0755 -d debian/libhts3t64/DEBIAN echo "libhts 3 libhts3t64 (>= 1.19+ds)" >> debian/libhts3t64/DEBIAN/shlibs chmod 0644 -- debian/libhts3t64/DEBIAN/shlibs dpkg-gensymbols -plibhts3t64 -Idebian/libhts3t64.symbols -Pdebian/libhts3t64 -edebian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 mv debian/.debhelper/generated/libhts3t64/triggers.new debian/.debhelper/generated/libhts3t64/triggers rm -f debian/libhts-dev/DEBIAN/shlibs rm -f debian/tabix/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/tabix/DEBIAN dpkg-shlibdeps -Tdebian/tabix.substvars debian/tabix/usr/bin/tabix debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/bgzip install -m0755 -d debian/libhts3t64/DEBIAN dpkg-shlibdeps -Tdebian/libhts3t64.substvars debian/libhts3t64/usr/lib/arm-linux-gnueabihf/libhts.so.1.19 debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb -a install -m0755 -d debian/libhts3t64/DEBIAN install -p -m0644 debian/.debhelper/generated/libhts3t64/triggers debian/libhts3t64/DEBIAN/triggers install -m0755 -d debian/libhts-dev/DEBIAN install -m0755 -d debian/tabix/DEBIAN dh_gencontrol -a install -m0755 -d debian/libhts3t64/DEBIAN echo misc:Depends= >> debian/libhts3t64.substvars echo misc:Pre-Depends= >> debian/libhts3t64.substvars install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -Pdebian/.debhelper/libhts3t64/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=libhts3t64-dbgsym "-DDepends=libhts3t64 (= \${binary:Version})" "-DDescription=debug symbols for libhts3t64" "-DBuild-Ids=000bf1efba4e77ba922732d940bb5924e4b32c39 04f9b674cb3cb5429bbbaddb3b185362f2d46e2f 16af9f42d7cf3f1d0b3b76d8620c81b472766554 7e7e25078afea2fe9c2c00abd4cf9493ea64da5b fd8dc793142324e15c6e76a383142e9c84259f07" -DSection=debug -DPackage-Type=ddeb -UReplaces -UBreaks install -m0755 -d debian/libhts-dev/DEBIAN echo misc:Depends= >> debian/libhts-dev.substvars echo misc:Pre-Depends= >> debian/libhts-dev.substvars dpkg-gencontrol -plibhts-dev -ldebian/changelog -Tdebian/libhts-dev.substvars -Pdebian/libhts-dev install -m0755 -d debian/tabix/DEBIAN echo misc:Depends= >> debian/tabix.substvars echo misc:Pre-Depends= >> debian/tabix.substvars install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/.debhelper/tabix/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=tabix-dbgsym "-DDepends=tabix (= \${binary:Version})" "-DDescription=debug symbols for tabix" "-DBuild-Ids=2d50a101dac9cdaabce2521bef11dab2845a2cf7 817fb5c936fb578fa4a64569093b524c3cab6108 bec9d1b3f9c28047364d2fed696efd8e601eebd6" -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: Provides field of package libhts3t64: substitution variable ${t64:Provides} used, but is not defined chmod 0644 -- debian/libhts-dev/DEBIAN/control chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -Pdebian/libhts3t64 dpkg-gencontrol: warning: Provides field of package libhts3t64: substitution variable ${t64:Provides} used, but is not defined chmod 0644 -- debian/tabix/DEBIAN/control chmod 0644 -- debian/libhts3t64/DEBIAN/control dh_md5sums -a install -m0755 -d debian/libhts3t64/DEBIAN install -m0755 -d debian/libhts-dev/DEBIAN install -m0755 -d debian/tabix/DEBIAN cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhts3t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts3t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN chmod 0644 -- debian/tabix/DEBIAN/md5sums install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN cd debian/.debhelper/libhts3t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --root-owner-group --build debian/libhts3t64 .. dpkg-deb --root-owner-group --build debian/libhts-dev .. dpkg-deb --root-owner-group --build debian/.debhelper/tabix/dbgsym-root debian/.debhelper/scratch-space/build-tabix INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libhts-dev (in debian/libhts-dev); do_strip: , oemstrip: pkgstriptranslations: processing libhts3t64 (in debian/libhts3t64); do_strip: , oemstrip: pkgstriptranslations: processing tabix-dbgsym (in debian/.debhelper/tabix/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libhts-dev/DEBIAN/control, package libhts-dev, directory debian/libhts-dev .. removing usr/share/doc/libhts-dev/changelog.gz INFO: pkgstripfiles: waiting for lock (libhts-dev) ... pkgstripfiles: processing control file: debian/libhts3t64/DEBIAN/control, package libhts3t64, directory debian/libhts3t64 .. removing usr/share/doc/libhts3t64/changelog.gz pkgstripfiles: Running PNG optimization (using 4 cpus) for package libhts3t64 ... pkgstripfiles: No PNG files. pkgstripfiles: processing control file: debian/.debhelper/tabix/dbgsym-root/DEBIAN/control, package tabix-dbgsym, directory debian/.debhelper/tabix/dbgsym-root dpkg-deb: building package 'tabix-dbgsym' in 'debian/.debhelper/scratch-space/build-tabix/tabix-dbgsym_1.19+ds-1.1build3_armhf.deb'. dpkg-deb: building package 'libhts3t64' in '../libhts3t64_1.19+ds-1.1build3_armhf.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/libhts3t64/dbgsym-root debian/.debhelper/scratch-space/build-libhts3t64 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libhts3t64-dbgsym (in debian/.debhelper/libhts3t64/dbgsym-root); do_strip: , oemstrip: Renaming tabix-dbgsym_1.19+ds-1.1build3_armhf.deb to tabix-dbgsym_1.19+ds-1.1build3_armhf.ddeb mv debian/.debhelper/scratch-space/build-tabix/tabix-dbgsym_1.19\+ds-1.1build3_armhf.deb ../tabix-dbgsym_1.19\+ds-1.1build3_armhf.ddeb pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com Searching for duplicated docs in dependency libhts3t64... symlinking changelog.Debian.gz in libhts-dev to file in libhts3t64 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libhts-dev ... pkgstripfiles: No PNG files. pkgstripfiles: processing control file: debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/control, package libhts3t64-dbgsym, directory debian/.debhelper/libhts3t64/dbgsym-root dpkg-deb: building package 'libhts3t64-dbgsym' in 'debian/.debhelper/scratch-space/build-libhts3t64/libhts3t64-dbgsym_1.19+ds-1.1build3_armhf.deb'. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.19+ds-1.1build3_armhf.deb'. Renaming libhts3t64-dbgsym_1.19+ds-1.1build3_armhf.deb to libhts3t64-dbgsym_1.19+ds-1.1build3_armhf.ddeb mv debian/.debhelper/scratch-space/build-libhts3t64/libhts3t64-dbgsym_1.19\+ds-1.1build3_armhf.deb ../libhts3t64-dbgsym_1.19\+ds-1.1build3_armhf.ddeb dpkg-deb --root-owner-group --build debian/tabix .. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing tabix (in debian/tabix); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/tabix/DEBIAN/control, package tabix, directory debian/tabix .. removing usr/share/doc/tabix/changelog.gz pkgstripfiles: Running PNG optimization (using 4 cpus) for package tabix ... pkgstripfiles: No PNG files. dpkg-deb: building package 'tabix' in '../tabix_1.19+ds-1.1build3_armhf.deb'. dpkg-genbuildinfo --build=any -O../htslib_1.19+ds-1.1build3_armhf.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../htslib_1.19+ds-1.1build3_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-source: info: using options from htslib-1.19+ds/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis\.yml|README.md|aclocal.m4|config.h.in|configure)$ dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-03-31T19:08:16Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ htslib_1.19+ds-1.1build3_armhf.changes: --------------------------------------- Format: 1.8 Date: Sun, 31 Mar 2024 18:25:58 +0000 Source: htslib Binary: libhts-dev libhts3t64 tabix Built-For-Profiles: noudeb Architecture: armhf Version: 1.19+ds-1.1build3 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: libhts-dev - development files for the HTSlib libhts3t64 - C library for high-throughput sequencing data formats tabix - generic indexer for TAB-delimited genome position files Changes: htslib (1.19+ds-1.1build3) noble; urgency=medium . * No-change rebuild for CVE-2024-3094 Checksums-Sha1: 29452716ba49f739547f7c82c66d413245139f04 7664 htslib_1.19+ds-1.1build3_armhf.buildinfo e0fa634715d3bc8852b7b0c61195af5de71a6887 1730742 libhts-dev_1.19+ds-1.1build3_armhf.deb 5ac9c355f2dd5b5591272afad8d1d01bcd1ad7f5 1239280 libhts3t64-dbgsym_1.19+ds-1.1build3_armhf.ddeb 6c39310dd561ec908bce55eadec21f72da0178cd 388654 libhts3t64_1.19+ds-1.1build3_armhf.deb 384757e1c7faaadca412831742b507522891ace2 2675844 tabix-dbgsym_1.19+ds-1.1build3_armhf.ddeb 4b7c618eebb48928a934e71c583367225de0cf01 427656 tabix_1.19+ds-1.1build3_armhf.deb Checksums-Sha256: 2cfe7363fba72de2c42079c5bc572fa2222f83af0d3dcc746cbb9b9551df8a09 7664 htslib_1.19+ds-1.1build3_armhf.buildinfo c90ce3b111cb16509dd4b1388a619a6d7e9a658d2d1057ce3ee17f2ba4492413 1730742 libhts-dev_1.19+ds-1.1build3_armhf.deb 739e380a1218342b18b987c0a17e271910063751dd7c2b76324fb55026f970d2 1239280 libhts3t64-dbgsym_1.19+ds-1.1build3_armhf.ddeb 60aded397e07c92a9707dc9c29f504e7fdc83e96e891a9876e429d0db9af39af 388654 libhts3t64_1.19+ds-1.1build3_armhf.deb 05a143a02cc6b3595f68b26182b5165c6b7a3ae31f0ea07952b43dbf2fb34e4a 2675844 tabix-dbgsym_1.19+ds-1.1build3_armhf.ddeb d8146e105475a0fe390f3785bd5a5269bd17cd809353eec2c289f1eeb844c857 427656 tabix_1.19+ds-1.1build3_armhf.deb Files: 50f9687abc624eb8f2413f1e2d99fb45 7664 science optional htslib_1.19+ds-1.1build3_armhf.buildinfo 89cc388b5d266b1bf5ecdb984b669aac 1730742 libdevel optional libhts-dev_1.19+ds-1.1build3_armhf.deb bd526290e18f9a48adacec2d54fb5531 1239280 debug optional libhts3t64-dbgsym_1.19+ds-1.1build3_armhf.ddeb 92d91914b27f89804195753b345a5c86 388654 libs optional libhts3t64_1.19+ds-1.1build3_armhf.deb 2c3aefff5d7a265083198838a3982da8 2675844 debug optional tabix-dbgsym_1.19+ds-1.1build3_armhf.ddeb afb0e9d89d1326bd225de0b50678a732 427656 science optional tabix_1.19+ds-1.1build3_armhf.deb Original-Maintainer: Debian Med Packaging Team /<>/htslib_1.19+ds-1.1build3_armhf.changes.new could not be renamed to /<>/htslib_1.19+ds-1.1build3_armhf.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: htslib Binary: libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: armhf Version: 1.19+ds-1.1build3 Checksums-Md5: 89cc388b5d266b1bf5ecdb984b669aac 1730742 libhts-dev_1.19+ds-1.1build3_armhf.deb bd526290e18f9a48adacec2d54fb5531 1239280 libhts3t64-dbgsym_1.19+ds-1.1build3_armhf.ddeb 92d91914b27f89804195753b345a5c86 388654 libhts3t64_1.19+ds-1.1build3_armhf.deb 2c3aefff5d7a265083198838a3982da8 2675844 tabix-dbgsym_1.19+ds-1.1build3_armhf.ddeb afb0e9d89d1326bd225de0b50678a732 427656 tabix_1.19+ds-1.1build3_armhf.deb Checksums-Sha1: e0fa634715d3bc8852b7b0c61195af5de71a6887 1730742 libhts-dev_1.19+ds-1.1build3_armhf.deb 5ac9c355f2dd5b5591272afad8d1d01bcd1ad7f5 1239280 libhts3t64-dbgsym_1.19+ds-1.1build3_armhf.ddeb 6c39310dd561ec908bce55eadec21f72da0178cd 388654 libhts3t64_1.19+ds-1.1build3_armhf.deb 384757e1c7faaadca412831742b507522891ace2 2675844 tabix-dbgsym_1.19+ds-1.1build3_armhf.ddeb 4b7c618eebb48928a934e71c583367225de0cf01 427656 tabix_1.19+ds-1.1build3_armhf.deb Checksums-Sha256: c90ce3b111cb16509dd4b1388a619a6d7e9a658d2d1057ce3ee17f2ba4492413 1730742 libhts-dev_1.19+ds-1.1build3_armhf.deb 739e380a1218342b18b987c0a17e271910063751dd7c2b76324fb55026f970d2 1239280 libhts3t64-dbgsym_1.19+ds-1.1build3_armhf.ddeb 60aded397e07c92a9707dc9c29f504e7fdc83e96e891a9876e429d0db9af39af 388654 libhts3t64_1.19+ds-1.1build3_armhf.deb 05a143a02cc6b3595f68b26182b5165c6b7a3ae31f0ea07952b43dbf2fb34e4a 2675844 tabix-dbgsym_1.19+ds-1.1build3_armhf.ddeb d8146e105475a0fe390f3785bd5a5269bd17cd809353eec2c289f1eeb844c857 427656 tabix_1.19+ds-1.1build3_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Sun, 31 Mar 2024 19:08:15 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu9), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-arm-linux-gnueabihf (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), bsdextrautils (= 2.39.3-9ubuntu3), bsdutils (= 1:2.39.3-9ubuntu3), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3ubuntu5), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-23ubuntu3), cpp-13-arm-linux-gnueabihf (= 13.2.0-23ubuntu3), cpp-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu5), debconf (= 1.5.86), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17build1), debugedit (= 1:5.0-5build1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6ubuntu6), dpkg-dev (= 1.22.6ubuntu6), dwz (= 0.15-1build5), file (= 1:5.45-3build1), findutils (= 4.9.0-5), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-23ubuntu3), g++-13-arm-linux-gnueabihf (= 13.2.0-23ubuntu3), g++-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-23ubuntu3), gcc-13-arm-linux-gnueabihf (= 13.2.0-23ubuntu3), gcc-13-base (= 13.2.0-23ubuntu3), gcc-14-base (= 14-20240330-1ubuntu2), gcc-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), grep (= 3.11-4), groff-base (= 1.23.0-3build2), gzip (= 1.12-1ubuntu2), hostname (= 3.23+nmu2ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240330-1ubuntu2), libatomic1 (= 14-20240330-1ubuntu2), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.1-1), libbinutils (= 2.42-4ubuntu2), libblkid1 (= 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(= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.0-20.20), login (= 1:4.13+dfsg1-4ubuntu1), lto-disabled-list (= 47), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-4build1), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), patch (= 2.7.6-7build2), perl (= 5.38.2-3.2build1), perl-base (= 5.38.2-3.2build1), perl-modules-5.38 (= 5.38.2-3.2build1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-6ubuntu2), tar (= 1.35+dfsg-3), util-linux (= 2.39.3-9ubuntu3), xz-utils (= 5.6.1+really5.4.5-1build1), 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="1711909558" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libhts-dev_1.19+ds-1.1build3_armhf.deb -------------------------------------- new Debian package, version 2.0. size 1730742 bytes: control archive=1914 bytes. 1311 bytes, 28 lines control 2202 bytes, 34 lines md5sums Package: libhts-dev Source: htslib Version: 1.19+ds-1.1build3 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 4672 Depends: libhts3t64 (= 1.19+ds-1.1build3), libcurl4-gnutls-dev, libdeflate-dev, liblzma-dev, zlib1g-dev Section: libdevel Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: development files for the HTSlib HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package contains development files for the HTSlib: headers, static library, manual pages, etc. . For compatibility with sambamba, the internal routine cram_to_bam was exported, hereto adopting a patch found in guix. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2024-03-31 18:25 ./ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/include/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/include/htslib/ -rw-r--r-- root/root 16469 2023-07-20 15:01 ./usr/include/htslib/bgzf.h -rw-r--r-- root/root 22175 2023-01-20 10:05 ./usr/include/htslib/cram.h -rw-r--r-- root/root 15122 2023-07-20 15:01 ./usr/include/htslib/faidx.h -rw-r--r-- root/root 13578 2023-09-08 16:43 ./usr/include/htslib/hfile.h -rw-r--r-- root/root 57362 2023-12-12 14:02 ./usr/include/htslib/hts.h -rw-r--r-- root/root 4307 2023-09-27 14:44 ./usr/include/htslib/hts_defs.h -rw-r--r-- root/root 11729 2023-08-24 15:40 ./usr/include/htslib/hts_endian.h -rw-r--r-- root/root 5991 2022-07-14 09:33 ./usr/include/htslib/hts_expr.h -rw-r--r-- root/root 3958 2022-05-13 15:25 ./usr/include/htslib/hts_log.h -rw-r--r-- root/root 2842 2022-01-11 12:11 ./usr/include/htslib/hts_os.h -rw-r--r-- root/root 5605 2020-01-23 10:28 ./usr/include/htslib/kbitset.h -rw-r--r-- root/root 2828 2019-11-19 11:20 ./usr/include/htslib/kfunc.h -rw-r--r-- root/root 22903 2023-04-06 07:36 ./usr/include/htslib/khash.h -rw-r--r-- root/root 4050 2020-08-10 08:46 ./usr/include/htslib/khash_str2int.h -rw-r--r-- root/root 5189 2023-10-03 15:40 ./usr/include/htslib/klist.h -rw-r--r-- root/root 3733 2022-07-27 10:31 ./usr/include/htslib/knetfile.h -rw-r--r-- root/root 3295 2020-08-27 10:09 ./usr/include/htslib/kroundup.h -rw-r--r-- root/root 9357 2023-10-03 15:40 ./usr/include/htslib/kseq.h -rw-r--r-- root/root 11507 2022-08-16 10:42 ./usr/include/htslib/ksort.h -rw-r--r-- root/root 11462 2022-07-27 10:31 ./usr/include/htslib/kstring.h -rw-r--r-- root/root 8881 2020-07-29 13:09 ./usr/include/htslib/regidx.h -rw-r--r-- root/root 92100 2023-11-11 17:07 ./usr/include/htslib/sam.h -rw-r--r-- root/root 16584 2023-06-05 14:19 ./usr/include/htslib/synced_bcf_reader.h -rw-r--r-- root/root 4956 2022-05-13 15:25 ./usr/include/htslib/tbx.h -rw-r--r-- root/root 12747 2020-09-16 09:17 ./usr/include/htslib/thread_pool.h -rw-r--r-- root/root 68936 2023-08-31 15:42 ./usr/include/htslib/vcf.h -rw-r--r-- root/root 1686 2020-07-11 11:34 ./usr/include/htslib/vcf_sweep.h -rw-r--r-- root/root 4919 2020-09-16 09:17 ./usr/include/htslib/vcfutils.h drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/ -rw-r--r-- root/root 4258066 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/libhts.a lrwxrwxrwx root/root 0 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/libhts.so -> libhts.so.1.19 drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/pkgconfig/ -rw-r--r-- root/root 728 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/pkgconfig/htslib.pc drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/doc/libhts-dev/ -rw-r--r-- root/root 2680 2021-04-12 09:37 ./usr/share/doc/libhts-dev/README -rw-r--r-- root/root 2961 2019-12-10 17:59 ./usr/share/doc/libhts-dev/README.large_positions.md.gz -rw-r--r-- root/root 401 2022-07-03 07:14 ./usr/share/doc/libhts-dev/README.test lrwxrwxrwx root/root 0 2024-03-31 18:25 ./usr/share/doc/libhts-dev/changelog.Debian.gz -> ../libhts3t64/changelog.Debian.gz -rw-r--r-- root/root 5897 2023-12-15 16:43 ./usr/share/doc/libhts-dev/copyright libhts3t64_1.19+ds-1.1build3_armhf.deb -------------------------------------- new Debian package, version 2.0. size 388654 bytes: control archive=6128 bytes. 1358 bytes, 24 lines control 897 bytes, 12 lines md5sums 33 bytes, 1 lines shlibs 30094 bytes, 929 lines symbols 75 bytes, 2 lines triggers Package: libhts3t64 Source: htslib Version: 1.19+ds-1.1build3 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 710 Depends: libbz2-1.0, libc6 (>= 2.34), libcurl3t64-gnutls (>= 7.18.0), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.3.0), liblzma5 (>= 5.1.1alpha+20120614), libssl3t64 (>= 3.0.0), zlib1g (>= 1:1.1.4) Breaks: ivar (<< 1.3.1~), libhts-dev (<< 1.13~), libhts3 (<< 1.19+ds-1.1build3), libtabixpp (<< 1.0.0-5~), samtools (<< 1.17~) Replaces: libhts-dev (<< 1.13~), libhts3 Section: libs Priority: optional Multi-Arch: same Homepage: https://github.com/samtools/htslib Description: C library for high-throughput sequencing data formats HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension ‘csi’ (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2024-03-31 18:25 ./ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/htslib/ -rw-r--r-- root/root 9668 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_gcs.so -rw-r--r-- root/root 17860 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_libcurl.so -rw-r--r-- root/root 22004 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_s3.so -rw-r--r-- root/root 13764 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/htslib/hfile_s3_write.so -rw-r--r-- root/root 554536 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/libhts.so.1.19 lrwxrwxrwx root/root 0 2024-03-31 18:25 ./usr/lib/arm-linux-gnueabihf/libhts.so.3 -> libhts.so.1.19 drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/doc/libhts3t64/ -rw-r--r-- root/root 3629 2024-03-31 18:25 ./usr/share/doc/libhts3t64/changelog.Debian.gz -rw-r--r-- root/root 5897 2023-12-15 16:43 ./usr/share/doc/libhts3t64/copyright drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 54 2024-02-28 10:38 ./usr/share/lintian/overrides/libhts3t64 drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/man/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/man/man5/ -rw-r--r-- root/root 2452 2024-03-31 18:25 ./usr/share/man/man5/faidx.5.gz -rw-r--r-- root/root 1537 2024-03-31 18:25 ./usr/share/man/man5/sam.5.gz -rw-r--r-- root/root 1857 2024-03-31 18:25 ./usr/share/man/man5/vcf.5.gz drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/man/man7/ -rw-r--r-- root/root 3419 2024-03-31 18:25 ./usr/share/man/man7/htslib-s3-plugin.7.gz tabix_1.19+ds-1.1build3_armhf.deb --------------------------------- new Debian package, version 2.0. size 427656 bytes: control archive=1055 bytes. 1072 bytes, 21 lines control 478 bytes, 8 lines md5sums Package: tabix Source: htslib Version: 1.19+ds-1.1build3 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 1449 Depends: libbz2-1.0, libc6 (>= 2.34), libdeflate0 (>= 1.0), libhtscodecs2 (>= 1.3.0), liblzma5 (>= 5.1.1alpha+20120614), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://github.com/samtools/htslib Description: generic indexer for TAB-delimited genome position files Tabix indexes files where some columns indicate sequence coordinates: name (usually a chromosome), start and stop. The input data file must be position sorted and compressed by bgzip (provided in this package), which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines by chromosomal coordinates. Fast data retrieval also works over network if an URI is given as a file name. . This package is built from the HTSlib source, and provides the bgzip, htsfile, and tabix tools. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2024-03-31 18:25 ./ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/bin/ -rwxr-xr-x root/root 411312 2024-03-31 18:25 ./usr/bin/bgzip -rwxr-xr-x root/root 497376 2024-03-31 18:25 ./usr/bin/htsfile -rwxr-xr-x root/root 509660 2024-03-31 18:25 ./usr/bin/tabix drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/doc/tabix/ -rw-r--r-- root/root 3627 2024-03-31 18:25 ./usr/share/doc/tabix/changelog.Debian.gz -rw-r--r-- root/root 5897 2023-12-15 16:43 ./usr/share/doc/tabix/copyright drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/man/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/share/man/man1/ -rw-r--r-- root/root 2958 2024-03-31 18:25 ./usr/share/man/man1/bgzip.1.gz -rw-r--r-- root/root 1919 2024-03-31 18:25 ./usr/share/man/man1/htsfile.1.gz -rw-r--r-- root/root 3341 2024-03-31 18:25 ./usr/share/man/man1/tabix.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 65068 Build-Time: 100 Distribution: noble-proposed Host Architecture: armhf Install-Time: 9 Job: htslib_1.19+ds-1.1build3.dsc Machine Architecture: arm64 Package: htslib Package-Time: 111 Source-Version: 1.19+ds-1.1build3 Space: 65068 Status: successful Version: 1.19+ds-1.1build3 -------------------------------------------------------------------------------- Finished at 2024-03-31T19:08:16Z Build needed 00:01:51, 65068k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27988872 Scanning for processes to kill in build PACKAGEBUILD-27988872