https://launchpad.net/ubuntu/+source/htslib/1.19+ds-1.1build3/+build/27988873 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-ppc64el-010 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:35 UTC 2024 ppc64le 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 23:11:26 ntpdate[1954]: adjust time server 10.211.37.1 offset 0.009026 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27988873 --image-type chroot /home/buildd/filecache-default/d42c54d6e204d222772cc047f01d282d9c30a0e5 Creating target for build PACKAGEBUILD-27988873 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27988873 Starting target for build PACKAGEBUILD-27988873 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27988873 '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-27988873 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27988873 Updating target for build PACKAGEBUILD-27988873 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 ppc64el Packages [1370 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el Packages [15.4 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6118 kB] Get:9 http://ftpmaster.internal/ubuntu noble-updates/main ppc64el Packages [683 kB] Get:10 http://ftpmaster.internal/ubuntu noble-updates/main Translation-en [242 kB] Get:11 http://ftpmaster.internal/ubuntu noble-updates/universe ppc64el Packages [4545 kB] Get:12 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [1693 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [528 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [204 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [1674 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [880 kB] Fetched 34.4 MB in 6s (5677 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-13-powerpc64le-linux-gnu gcc-14-base gcc-powerpc64le-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages have been kept back: libaudit1 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-powerpc64le-linux-gnu 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 libitm1 libjansson4 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 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 157 upgraded, 23 newly installed, 14 to remove and 1 not upgraded. Need to get 118 MB of archives. After this operation, 83.6 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnsl-dev ppc64el 1.3.0-3build3 [80.3 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [167 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc6-dev ppc64el 2.39-0ubuntu8 [2104 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-dev-bin ppc64el 2.39-0ubuntu8 [21.3 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1.1build1 [225 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libnss-nisplus ppc64el 1.3-5 [27.4 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtirpc3t64 ppc64el 1.3.4+ds-1.1build1 [102 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgssapi-krb5-2 ppc64el 1.20.1-6ubuntu2 [185 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkrb5-3 ppc64el 1.20.1-6ubuntu2 [432 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libk5crypto3 ppc64el 1.20.1-6ubuntu2 [108 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkrb5support0 ppc64el 1.20.1-6ubuntu2 [38.6 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libacl1 ppc64el 2.3.2-1 [21.4 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libapparmor1 ppc64el 4.0.0-beta3-0ubuntu3 [55.1 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libblkid1 ppc64el 2.39.3-9ubuntu3 [155 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libcap2 ppc64el 1:2.66-5ubuntu1 [35.6 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libcrypt1 ppc64el 1:4.4.36-4 [125 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el libgpg-error-l10n all 1.47-3build1 [8024 B] Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el libgpg-error0 ppc64el 1.47-3build1 [87.6 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libgcrypt20 ppc64el 1.10.3-2 [745 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblzma5 ppc64el 5.6.1+really5.4.5-1build1 [160 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el libzstd1 ppc64el 1.5.5+dfsg2-2 [390 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libkmod2 ppc64el 31+20240202-2ubuntu5 [64.4 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libpcre2-8-0 ppc64el 10.42-4ubuntu1 [263 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libselinux1 ppc64el 3.5-2ubuntu2 [101 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmount1 ppc64el 2.39.3-9ubuntu3 [169 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-modules-5.38 all 5.38.2-3.2build1 [3110 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdb5.3t64 ppc64el 5.3.28+dfsg2-6build1 [869 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm6t64 ppc64el 1.23-5.1build1 [42.0 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgdbm-compat4t64 ppc64el 1.23-5.1build1 [6982 B] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libperl5.38t64 ppc64el 5.38.2-3.2build1 [4962 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl ppc64el 5.38.2-3.2build1 [231 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el perl-base ppc64el 5.38.2-3.2build1 [1916 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblocale-gettext-perl ppc64el 1.07-6ubuntu5 [16.1 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtext-iconv-perl ppc64el 1.7-8build3 [13.7 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtext-charwidth-perl ppc64el 0.04-11build3 [9536 B] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc6 ppc64el 2.39-0ubuntu8 [3275 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libc-bin ppc64el 2.39-0ubuntu8 [751 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el openssl ppc64el 3.0.13-0ubuntu3 [1025 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libsystemd-shared ppc64el 255.4-1ubuntu5 [2351 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcryptsetup12 ppc64el 2:2.7.0-1ubuntu3 [376 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl3t64 ppc64el 3.0.13-0ubuntu3 [2125 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el systemd-dev all 255.4-1ubuntu6 [104 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el systemd-sysv ppc64el 255.4-1ubuntu5 [11.9 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main ppc64el systemd ppc64el 255.4-1ubuntu5 [3771 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main ppc64el libsystemd0 ppc64el 255.4-1ubuntu5 [526 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-modules-bin ppc64el 1.5.3-5ubuntu4 [57.9 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-modules ppc64el 1.5.3-5ubuntu4 [320 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnettle8t64 ppc64el 3.9.1-2.2build1 [226 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libhogweed6t64 ppc64el 3.9.1-2.2build1 [208 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main ppc64el libp11-kit0 ppc64el 0.25.3-4ubuntu1 [315 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main ppc64el libunistring5 ppc64el 1.1-2 [556 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgnutls30t64 ppc64el 3.8.3-1.1ubuntu3 [1055 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main ppc64el libapt-pkg6.0t64 ppc64el 2.7.14 [1063 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bzip2 ppc64el 1.0.8-5.1 [37.6 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbz2-1.0 ppc64el 1.0.8-5.1 [48.7 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-14-base ppc64el 14-20240330-1ubuntu2 [47.5 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgcc-s1 ppc64el 14-20240330-1ubuntu2 [39.3 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libstdc++6 ppc64el 14-20240330-1ubuntu2 [893 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main ppc64el libudev1 ppc64el 255.4-1ubuntu5 [200 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main ppc64el libxxhash0 ppc64el 0.8.2-2 [30.4 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el zlib1g ppc64el 1:1.3.dfsg-3.1ubuntu2 [72.8 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main ppc64el libffi8 ppc64el 3.4.6-1 [27.7 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main ppc64el libidn2-0 ppc64el 2.3.7-2 [69.8 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdebconfclient0 ppc64el 0.271ubuntu3 [11.3 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main ppc64el base-passwd ppc64el 3.6.3 [52.5 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsqlite3-0 ppc64el 3.45.1-1ubuntu2 [804 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg ppc64el 2.4.4-2ubuntu16 [706 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libreadline8t64 ppc64el 8.2-4build1 [182 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el readline-common all 8.2-4build1 [56.5 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main ppc64el libncursesw6 ppc64el 6.4+20240113-1ubuntu1 [186 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main ppc64el libtinfo6 ppc64el 6.4+20240113-1ubuntu1 [129 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpg-agent ppc64el 2.4.4-2ubuntu16 [275 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgconf ppc64el 2.4.4-2ubuntu16 [115 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main ppc64el pinentry-curses ppc64el 1.2.1-3ubuntu4 [38.7 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main ppc64el init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnpth0t64 ppc64el 1.6-3.1build1 [8914 B] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gpgv ppc64el 2.4.4-2ubuntu16 [198 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main ppc64el ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libseccomp2 ppc64el 2.5.5-1ubuntu3 [62.5 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main ppc64el apt-utils ppc64el 2.7.14 [226 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main ppc64el apt ppc64el 2.7.14 [1401 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main ppc64el debconf-i18n all 1.5.86 [205 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main ppc64el debconf all 1.5.86 [124 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam0g ppc64el 1.5.3-5ubuntu4 [75.8 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main ppc64el libargon2-1 ppc64el 0~20190702+dfsg-4 [27.1 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdevmapper1.02.1 ppc64el 2:1.02.185-3ubuntu3 [182 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libuuid1 ppc64el 2.39.3-9ubuntu3 [39.5 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfdisk1 ppc64el 2.39.3-9ubuntu3 [171 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el mount ppc64el 2.39.3-9ubuntu3 [125 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcom-err2 ppc64el 1.47.0-2.4~exp1ubuntu3 [22.9 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main ppc64el libkeyutils1 ppc64el 1.6.3-3 [11.0 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnsl2 ppc64el 1.3.0-3build3 [48.9 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main ppc64el linux-libc-dev ppc64el 6.8.0-20.20 [1586 kB] Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el base-files ppc64el 13ubuntu9 [74.0 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el debianutils ppc64el 5.17build1 [90.5 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bash ppc64el 5.2.21-2ubuntu4 [977 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bsdutils ppc64el 1:2.39.3-9ubuntu3 [99.0 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el coreutils ppc64el 9.4-3ubuntu5 [1523 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main ppc64el tar ppc64el 1.35+dfsg-3 [307 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dpkg ppc64el 1.22.6ubuntu6 [1343 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dash ppc64el 0.5.12-6ubuntu5 [108 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main ppc64el diffutils ppc64el 1:3.10-1 [200 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main ppc64el grep ppc64el 3.11-4 [189 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main ppc64el gzip ppc64el 1.12-1ubuntu2 [114 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main ppc64el hostname ppc64el 3.23+nmu2ubuntu1 [11.3 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main ppc64el login ppc64el 1:4.13+dfsg1-4ubuntu1 [205 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main ppc64el ncurses-bin ppc64el 6.4+20240113-1ubuntu1 [202 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main ppc64el sed ppc64el 4.9-2 [223 kB] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el util-linux ppc64el 2.39.3-9ubuntu3 [1195 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main ppc64el ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main ppc64el sysvinit-utils ppc64el 3.08-6ubuntu2 [35.7 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el logsave ppc64el 1.47.0-2.4~exp1ubuntu3 [23.0 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libext2fs2t64 ppc64el 1.47.0-2.4~exp1ubuntu3 [270 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el e2fsprogs ppc64el 1.47.0-2.4~exp1ubuntu3 [663 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el optipng ppc64el 0.7.8+ds-1build2 [118 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpng16-16t64 ppc64el 1.6.43-5build1 [242 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main ppc64el init ppc64el 1.66ubuntu1 [6190 B] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsmartcols1 ppc64el 2.39.3-9ubuntu3 [79.2 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el uuid-runtime ppc64el 2.39.3-9ubuntu3 [33.8 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main ppc64el libattr1 ppc64el 1:2.5.2-1 [12.4 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main ppc64el libaudit-common all 1:3.1.2-2.1 [5674 B] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcap-ng0 ppc64el 0.8.4-2build2 [16.3 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main ppc64el libmd0 ppc64el 1.1.0-2 [30.4 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main ppc64el libsemanage-common all 3.5-1build4 [10.1 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main ppc64el libsepol2 ppc64el 3.5-2 [386 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main ppc64el libsemanage2 ppc64el 3.5-1build4 [115 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main ppc64el passwd ppc64el 1:4.13+dfsg1-4ubuntu1 [878 kB] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libproc2-0 ppc64el 2:4.0.4-4ubuntu3 [68.7 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libss2 ppc64el 1.47.0-2.4~exp1ubuntu3 [18.0 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main ppc64el mawk ppc64el 1.3.4.20240123-1 [138 kB] Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el procps ppc64el 2:4.0.4-4ubuntu3 [736 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main ppc64el sensible-utils all 0.0.22 [22.5 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main ppc64el ca-certificates all 20240203 [159 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main ppc64el krb5-locales all 1.20.1-6ubuntu1 [13.8 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main ppc64el tzdata all 2024a-1ubuntu1 [273 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main ppc64el bash-completion all 1:2.11-8 [180 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el bsdextrautils ppc64el 2.39.3-9ubuntu3 [78.6 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgpm2 ppc64el 1.20.7-11 [15.9 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main ppc64el libip4tc2 ppc64el 1.8.10-3ubuntu1 [26.9 kB] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libjansson4 ppc64el 2.14-2build2 [40.4 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el psmisc ppc64el 23.7-1build1 [192 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el xz-utils ppc64el 5.6.1+really5.4.5-1build1 [276 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main ppc64el libctf0 ppc64el 2.42-4ubuntu2 [112 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main ppc64el libctf-nobfd0 ppc64el 2.42-4ubuntu2 [112 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.42-4ubuntu2 [2473 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main ppc64el libbinutils ppc64el 2.42-4ubuntu2 [699 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main ppc64el binutils ppc64el 2.42-4ubuntu2 [3080 B] Get:150 http://ftpmaster.internal/ubuntu noble/main ppc64el binutils-common ppc64el 2.42-4ubuntu2 [217 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main ppc64el libsframe1 ppc64el 2.42-4ubuntu2 [16.0 kB] Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libubsan1 ppc64el 14-20240330-1ubuntu2 [1194 kB] Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el g++-13 ppc64el 13.2.0-23ubuntu3 [14.5 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libstdc++-13-dev ppc64el 13.2.0-23ubuntu3 [2510 kB] Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgomp1 ppc64el 14-20240330-1ubuntu2 [161 kB] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libitm1 ppc64el 14-20240330-1ubuntu2 [32.3 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libatomic1 ppc64el 14-20240330-1ubuntu2 [10.7 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libasan8 ppc64el 14-20240330-1ubuntu2 [2973 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblsan0 ppc64el 14-20240330-1ubuntu2 [1325 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libquadmath0 ppc64el 14-20240330-1ubuntu2 [158 kB] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-13 ppc64el 13.2.0-23ubuntu3 [479 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libgcc-13-dev ppc64el 13.2.0-23ubuntu3 [1579 kB] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libtsan2 ppc64el 14-20240330-1ubuntu2 [2700 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcc1-0 ppc64el 14-20240330-1ubuntu2 [48.4 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el cpp-13 ppc64el 13.2.0-23ubuntu3 [1036 B] Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-13-base ppc64el 13.2.0-23ubuntu3 [48.7 kB] Get:167 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el gcc-13-powerpc64le-linux-gnu ppc64el 13.2.0-23ubuntu3 [20.6 MB] Get:168 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el g++-13-powerpc64le-linux-gnu ppc64el 13.2.0-23ubuntu3 [12.2 MB] Get:169 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el cpp-13-powerpc64le-linux-gnu ppc64el 13.2.0-23ubuntu3 [10.7 MB] Get:170 http://ftpmaster.internal/ubuntu noble/main ppc64el g++ ppc64el 4:13.2.0-7ubuntu1 [1086 B] Get:171 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc ppc64el 4:13.2.0-7ubuntu1 [5022 B] Get:172 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp ppc64el 4:13.2.0-7ubuntu1 [22.5 kB] Get:173 http://ftpmaster.internal/ubuntu noble/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [5330 B] Get:174 http://ftpmaster.internal/ubuntu noble/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [1224 B] Get:175 http://ftpmaster.internal/ubuntu noble/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:13.2.0-7ubuntu1 [968 B] Get:176 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:178 http://ftpmaster.internal/ubuntu noble/main ppc64el lto-disabled-list all 47 [12.4 kB] Get:179 http://ftpmaster.internal/ubuntu noble/main ppc64el libfakeroot ppc64el 1.33-1 [34.4 kB] Get:180 http://ftpmaster.internal/ubuntu noble/main ppc64el fakeroot ppc64el 1.33-1 [69.2 kB] Preconfiguring packages ... Fetched 118 MB in 5s (23.5 MB/s) (Reading database ... 13550 files and directories currently installed.) Preparing to unpack .../0-libnsl-dev_1.3.0-3build3_ppc64el.deb ... Unpacking libnsl-dev:ppc64el (1.3.0-3build3) over (1.3.0-2build2) ... Preparing to unpack .../1-libcrypt-dev_1%3a4.4.36-4_ppc64el.deb ... Unpacking libcrypt-dev:ppc64el (1:4.4.36-4) over (1:4.4.36-2) ... Preparing to unpack .../2-libc6-dev_2.39-0ubuntu8_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Preparing to unpack .../3-libc-dev-bin_2.39-0ubuntu8_ppc64el.deb ... Unpacking libc-dev-bin (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Preparing to unpack .../4-libtirpc-common_1.3.4+ds-1.1build1_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.1build1) over (1.3.3+ds-1) ... Preparing to unpack .../5-libtirpc-dev_1.3.4+ds-1.1build1_ppc64el.deb ... Unpacking libtirpc-dev:ppc64el (1.3.4+ds-1.1build1) over (1.3.3+ds-1) ... Preparing to unpack .../6-libnss-nisplus_1.3-5_ppc64el.deb ... Unpacking libnss-nisplus:ppc64el (1.3-5) over (1.3-0ubuntu6) ... dpkg: libtirpc3:ppc64el: dependency problems, but removing anyway as you requested: libnsl2:ppc64el depends on libtirpc3 (>= 1.0.2). (Reading database ... 13553 files and directories currently installed.) Removing libtirpc3:ppc64el (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3t64:ppc64el. (Reading database ... 13547 files and directories currently installed.) Preparing to unpack .../0-libtirpc3t64_1.3.4+ds-1.1build1_ppc64el.deb ... Adding 'diversion of /lib/powerpc64le-linux-gnu/libtirpc.so.3 to /lib/powerpc64le-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/powerpc64le-linux-gnu/libtirpc.so.3.0.0 to /lib/powerpc64le-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:ppc64el (1.3.4+ds-1.1build1) ... Preparing to unpack .../1-libgssapi-krb5-2_1.20.1-6ubuntu2_ppc64el.deb ... 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Setting up libgpg-error0:ppc64el (1.47-3build1) ... (Reading database ... 13558 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.3-2_ppc64el.deb ... Unpacking libgcrypt20:ppc64el (1.10.3-2) over (1.10.2-3ubuntu1) ... Setting up libgcrypt20:ppc64el (1.10.3-2) ... (Reading database ... 13558 files and directories currently installed.) Preparing to unpack .../liblzma5_5.6.1+really5.4.5-1build1_ppc64el.deb ... Unpacking liblzma5:ppc64el (5.6.1+really5.4.5-1build1) over (5.4.1-0.2) ... Setting up liblzma5:ppc64el (5.6.1+really5.4.5-1build1) ... (Reading database ... 13558 files and directories currently installed.) Preparing to unpack .../libzstd1_1.5.5+dfsg2-2_ppc64el.deb ... Unpacking libzstd1:ppc64el (1.5.5+dfsg2-2) over (1.5.5+dfsg2-1ubuntu2) ... Setting up libzstd1:ppc64el (1.5.5+dfsg2-2) ... (Reading database ... 13558 files and directories currently installed.) Preparing to unpack .../libkmod2_31+20240202-2ubuntu5_ppc64el.deb ... 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Selecting previously unselected package perl-modules-5.38. Preparing to unpack .../perl-modules-5.38_5.38.2-3.2build1_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3.2build1) ... dpkg: libdb5.3:ppc64el: dependency problems, but removing anyway as you requested: libperl5.36:ppc64el depends on libdb5.3. libpam-modules:ppc64el depends on libdb5.3. apt-utils depends on libdb5.3. (Reading database ... 14971 files and directories currently installed.) Removing libdb5.3:ppc64el (5.3.28+dfsg2-2) ... Selecting previously unselected package libdb5.3t64:ppc64el. (Reading database ... 14965 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6build1_ppc64el.deb ... Unpacking libdb5.3t64:ppc64el (5.3.28+dfsg2-6build1) ... dpkg: libgdbm6:ppc64el: dependency problems, but removing anyway as you requested: libperl5.36:ppc64el depends on libgdbm6 (>= 1.21). libgdbm-compat4:ppc64el depends on libgdbm6 (>= 1.16). (Reading database ... 14971 files and directories currently installed.) Removing libgdbm6:ppc64el (1.23-3) ... Selecting previously unselected package libgdbm6t64:ppc64el. (Reading database ... 14966 files and directories currently installed.) Preparing to unpack .../libgdbm6t64_1.23-5.1build1_ppc64el.deb ... Unpacking libgdbm6t64:ppc64el (1.23-5.1build1) ... dpkg: libgdbm-compat4:ppc64el: dependency problems, but removing anyway as you requested: libperl5.36:ppc64el depends on libgdbm-compat4 (>= 1.18-3). (Reading database ... 14972 files and directories currently installed.) Removing libgdbm-compat4:ppc64el (1.23-3) ... Selecting previously unselected package libgdbm-compat4t64:ppc64el. (Reading database ... 14967 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4t64_1.23-5.1build1_ppc64el.deb ... Unpacking libgdbm-compat4t64:ppc64el (1.23-5.1build1) ... Selecting previously unselected package libperl5.38t64:ppc64el. Preparing to unpack .../libperl5.38t64_5.38.2-3.2build1_ppc64el.deb ... Unpacking libperl5.38t64:ppc64el (5.38.2-3.2build1) ... Preparing to unpack .../perl-base_5.38.2-3.2build1_ppc64el.deb ... Unpacking perl-base (5.38.2-3.2build1) over (5.36.0-9ubuntu1) ... Setting up perl-base (5.38.2-3.2build1) ... (Reading database ... 15499 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu5_ppc64el.deb ... Unpacking liblocale-gettext-perl (1.07-6ubuntu5) over (1.07-6) ... Preparing to unpack .../libtext-iconv-perl_1.7-8build3_ppc64el.deb ... Unpacking libtext-iconv-perl:ppc64el (1.7-8build3) over (1.7-8) ... Preparing to unpack .../libtext-charwidth-perl_0.04-11build3_ppc64el.deb ... Unpacking libtext-charwidth-perl:ppc64el (0.04-11build3) over (0.04-11) ... Preparing to unpack .../libc6_2.39-0ubuntu8_ppc64el.deb ... Unpacking libc6:ppc64el (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Setting up libc6:ppc64el (2.39-0ubuntu8) ... (Reading database ... 15503 files and directories currently installed.) Preparing to unpack .../libc-bin_2.39-0ubuntu8_ppc64el.deb ... Unpacking libc-bin (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Setting up libc-bin (2.39-0ubuntu8) ... (Reading database ... 15503 files and directories currently installed.) Preparing to unpack .../openssl_3.0.13-0ubuntu3_ppc64el.deb ... Unpacking openssl (3.0.13-0ubuntu3) over (3.0.10-1ubuntu2) ... Preparing to unpack .../libsystemd-shared_255.4-1ubuntu5_ppc64el.deb ... Unpacking libsystemd-shared:ppc64el (255.4-1ubuntu5) over (253.5-1ubuntu6) ... Preparing to unpack .../libcryptsetup12_2%3a2.7.0-1ubuntu3_ppc64el.deb ... Unpacking libcryptsetup12:ppc64el (2:2.7.0-1ubuntu3) over (2:2.6.1-4ubuntu3) ... dpkg: libssl3:ppc64el: dependency problems, but removing anyway as you requested: systemd depends on libssl3 (>= 3.0.0). (Reading database ... 15502 files and directories currently installed.) Removing libssl3:ppc64el (3.0.10-1ubuntu2) ... Selecting previously unselected package libssl3t64:ppc64el. (Reading database ... 15491 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.0.13-0ubuntu3_ppc64el.deb ... Unpacking libssl3t64:ppc64el (3.0.13-0ubuntu3) ... Setting up libssl3t64:ppc64el (3.0.13-0ubuntu3) ... (Reading database ... 15504 files and directories currently installed.) Preparing to unpack .../systemd-dev_255.4-1ubuntu6_all.deb ... Unpacking systemd-dev (255.4-1ubuntu6) over (253.5-1ubuntu6) ... Preparing to unpack .../systemd-sysv_255.4-1ubuntu5_ppc64el.deb ... Unpacking systemd-sysv (255.4-1ubuntu5) over (253.5-1ubuntu6) ... Preparing to unpack .../systemd_255.4-1ubuntu5_ppc64el.deb ... Unpacking systemd (255.4-1ubuntu5) over (253.5-1ubuntu6) ... dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sockets.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/multi-user.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/journald.conf.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty Preparing to unpack .../libsystemd0_255.4-1ubuntu5_ppc64el.deb ... Unpacking libsystemd0:ppc64el (255.4-1ubuntu5) over (253.5-1ubuntu6) ... Setting up libsystemd0:ppc64el (255.4-1ubuntu5) ... (Reading database ... 15643 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu4_ppc64el.deb ... Unpacking libpam-modules-bin (1.5.3-5ubuntu4) over (1.5.2-6ubuntu1) ... Setting up libpam-modules-bin (1.5.3-5ubuntu4) ... (Reading database ... 15642 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-5ubuntu4_ppc64el.deb ... Unpacking libpam-modules:ppc64el (1.5.3-5ubuntu4) over (1.5.2-6ubuntu1) ... dpkg: warning: unable to delete old directory '/lib/powerpc64le-linux-gnu/security': Directory not empty Setting up libpam-modules:ppc64el (1.5.3-5ubuntu4) ... Installing new version of config file /etc/security/namespace.init ... dpkg: libhogweed6:ppc64el: dependency problems, but removing anyway as you requested: libgnutls30:ppc64el depends on libhogweed6 (>= 3.6). (Reading database ... 15639 files and directories currently installed.) Removing libhogweed6:ppc64el (3.9.1-2) ... dpkg: libnettle8:ppc64el: dependency problems, but removing anyway as you requested: libgnutls30:ppc64el depends on libnettle8 (>= 3.7~). Removing libnettle8:ppc64el (3.9.1-2) ... Selecting previously unselected package libnettle8t64:ppc64el. (Reading database ... 15627 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.9.1-2.2build1_ppc64el.deb ... Unpacking libnettle8t64:ppc64el (3.9.1-2.2build1) ... Setting up libnettle8t64:ppc64el (3.9.1-2.2build1) ... Selecting previously unselected package libhogweed6t64:ppc64el. (Reading database ... 15635 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2build1_ppc64el.deb ... Unpacking libhogweed6t64:ppc64el (3.9.1-2.2build1) ... Setting up libhogweed6t64:ppc64el (3.9.1-2.2build1) ... (Reading database ... 15641 files and directories currently installed.) 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(both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') Preparing to unpack .../libbz2-1.0_1.0.8-5.1_ppc64el.deb ... Unpacking libbz2-1.0:ppc64el (1.0.8-5.1) over (1.0.8-5build1) ... Setting up libbz2-1.0:ppc64el (1.0.8-5.1) ... Selecting previously unselected package gcc-14-base:ppc64el. (Reading database ... 15649 files and directories currently installed.) 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(Reading database ... 15654 files and directories currently installed.) Removing libreadline8:ppc64el (8.2-1.3) ... Selecting previously unselected package libreadline8t64:ppc64el. (Reading database ... 15642 files and directories currently installed.) Preparing to unpack .../libreadline8t64_8.2-4build1_ppc64el.deb ... Adding 'diversion of /lib/powerpc64le-linux-gnu/libhistory.so.8 to /lib/powerpc64le-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/powerpc64le-linux-gnu/libhistory.so.8.2 to /lib/powerpc64le-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/powerpc64le-linux-gnu/libreadline.so.8 to /lib/powerpc64le-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/powerpc64le-linux-gnu/libreadline.so.8.2 to /lib/powerpc64le-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:ppc64el (8.2-4build1) ... 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Setting up bsdextrautils (2.39.3-9ubuntu3) ... Setting up init (1.66ubuntu1) ... Setting up libgdbm-compat4t64:ppc64el (1.23-5.1build1) ... Setting up psmisc (23.7-1build1) ... Setting up libtirpc-common (1.3.4+ds-1.1build1) ... Setting up libsqlite3-0:ppc64el (3.45.1-1ubuntu2) ... Setting up binutils-common:ppc64el (2.42-4ubuntu2) ... Setting up linux-libc-dev:ppc64el (6.8.0-20.20) ... Setting up libctf-nobfd0:ppc64el (2.42-4ubuntu2) ... Setting up krb5-locales (1.20.1-6ubuntu1) ... Setting up libgomp1:ppc64el (14-20240330-1ubuntu2) ... Setting up bzip2 (1.0.8-5.1) ... Setting up libsframe1:ppc64el (2.42-4ubuntu2) ... Setting up libfakeroot:ppc64el (1.33-1) ... Setting up libjansson4:ppc64el (2.14-2build2) ... Setting up libkrb5support0:ppc64el (1.20.1-6ubuntu2) ... Setting up tzdata (2024a-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Mar 31 23:12:00 UTC 2024. Universal Time is now: Sun Mar 31 23:12:00 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... Setting up gcc-13-base:ppc64el (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 libquadmath0:ppc64el (14-20240330-1ubuntu2) ... Setting up libproc2-0:ppc64el (2:4.0.4-4ubuntu3) ... Setting up libpng16-16t64:ppc64el (1.6.43-5build1) ... Setting up libatomic1:ppc64el (14-20240330-1ubuntu2) ... Setting up libss2:ppc64el (1.47.0-2.4~exp1ubuntu3) ... Setting up libncursesw6:ppc64el (6.4+20240113-1ubuntu1) ... Setting up libk5crypto3:ppc64el (1.20.1-6ubuntu2) ... Setting up logsave (1.47.0-2.4~exp1ubuntu3) ... Setting up libdb5.3t64:ppc64el (5.3.28+dfsg2-6build1) ... Setting up libubsan1:ppc64el (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. Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... Setting up libasan8:ppc64el (14-20240330-1ubuntu2) ... Setting up procps (2:4.0.4-4ubuntu3) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:ppc64el (1.20.1-6ubuntu2) ... Setting up libperl5.38t64:ppc64el (5.38.2-3.2build1) ... Setting up libtsan2:ppc64el (14-20240330-1ubuntu2) ... Setting up libbinutils:ppc64el (2.42-4ubuntu2) ... Setting up libc-dev-bin (2.39-0ubuntu8) ... Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-23ubuntu3) ... Setting up openssl (3.0.13-0ubuntu3) ... Setting up libgpg-error-l10n (1.47-3build1) ... Setting up readline-common (8.2-4build1) ... Setting up libcc1-0:ppc64el (14-20240330-1ubuntu2) ... Setting up liblocale-gettext-perl (1.07-6ubuntu5) ... Setting up liblsan0:ppc64el (14-20240330-1ubuntu2) ... Setting up libitm1:ppc64el (14-20240330-1ubuntu2) ... Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libctf0:ppc64el (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu4) ... Setting up apt-utils (2.7.14) ... Setting up cpp-13 (13.2.0-23ubuntu3) ... Setting up debconf-i18n (1.5.86) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu3) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-3.2build1) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up libgssapi-krb5-2:ppc64el (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu6) ... Setting up libreadline8t64:ppc64el (8.2-4build1) ... Setting up libgcc-13-dev:ppc64el (13.2.0-23ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu16) ... Setting up libc6-dev:ppc64el (2.39-0ubuntu8) ... Setting up binutils-powerpc64le-linux-gnu (2.42-4ubuntu2) ... Setting up gpg (2.4.4-2ubuntu16) ... Setting up libstdc++-13-dev:ppc64el (13.2.0-23ubuntu3) ... Setting up gpg-agent (2.4.4-2ubuntu16) ... Setting up libtirpc3t64:ppc64el (1.3.4+ds-1.1build1) ... Setting up binutils (2.42-4ubuntu2) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:ppc64el (1.3.4+ds-1.1build1) ... Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-13 (13.2.0-23ubuntu3) ... Setting up libnsl2:ppc64el (1.3.0-3build3) ... Setting up libnss-nisplus:ppc64el (1.3-5) ... Setting up g++-13-powerpc64le-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:ppc64el (1.3.0-3build3) ... Setting up g++-powerpc64le-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu3) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15707 files and directories currently installed.) Purging configuration files for libssl3:ppc64el (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-27988873 ppc64el noble-proposed -c chroot:build-PACKAGEBUILD-27988873 --arch=ppc64el --dist=noble-proposed --nolog htslib_1.19+ds-1.1build3.dsc Initiating build PACKAGEBUILD-27988873 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:35 UTC 2024 ppc64le sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-ppc64el-010.buildd +==============================================================================+ | htslib 1.19+ds-1.1build3 (ppc64el) Sun, 31 Mar 2024 23:12:04 +0000 | +==============================================================================+ Package: htslib Version: 1.19+ds-1.1build3 Source Version: 1.19+ds-1.1build3 Distribution: noble-proposed Machine Architecture: ppc64el Host Architecture: ppc64el Build Architecture: ppc64el Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27988873/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/htslib-D6ec71/resolver-rK4wCb' 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-D6ec71/htslib-1.19+ds' with '<>' I: NOTICE: Log filtering will replace 'build/htslib-D6ec71' 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 (178 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 libperl5.36 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 29.0 MB of archives. After this operation, 105 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 ppc64el libelf1t64 ppc64el 0.190-1.1build3 [69.3 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libicu74 ppc64el 74.2-1ubuntu1 [11.3 MB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libxml2 ppc64el 2.9.14+dfsg-1.3ubuntu3 [840 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmagic-mgc ppc64el 1:5.45-3build1 [307 kB] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libmagic1t64 ppc64el 1:5.45-3build1 [106 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el file ppc64el 1:5.45-3build1 [22.7 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el gettext-base ppc64el 0.21-14ubuntu1 [42.7 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libuchardet0 ppc64el 0.0.8-1 [78.7 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el groff-base ppc64el 1.23.0-3build2 [1112 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libnghttp2-14 ppc64el 1.59.0-1build2 [89.1 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpipeline1 ppc64el 1.5.7-2 [26.9 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libpsl5t64 ppc64el 0.21.2-1.1build1 [59.1 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el man-db ppc64el 2.12.0-4build1 [1281 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el m4 ppc64el 1.4.19-4 [275 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el autoconf all 2.71-3 [339 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el autotools-dev all 20220109.1 [44.9 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el autopoint all 0.21-14ubuntu1 [422 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libtool all 2.4.7-7 [166 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-autoreconf all 20 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main ppc64el libsub-override-perl all 0.10-1 [10.0 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main ppc64el libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main ppc64el dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libdw1t64 ppc64el 0.190-1.1build3 [301 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el debugedit ppc64el 1:5.0-5build1 [51.4 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el dwz ppc64el 0.15-1build5 [142 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el gettext ppc64el 0.21-14ubuntu1 [979 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main ppc64el debhelper all 13.14.1ubuntu5 [869 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main ppc64el libbrotli1 ppc64el 1.1.0-2build1 [410 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libbz2-dev ppc64el 1.0.8-5.1 [51.2 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsasl2-modules-db ppc64el 2.1.28+dfsg1-5ubuntu2 [23.4 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libsasl2-2 ppc64el 2.1.28+dfsg1-5ubuntu2 [68.0 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libldap2 ppc64el 2.6.7+dfsg-1~exp1ubuntu7 [233 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d.1-2build7 [64.4 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main ppc64el libssh-4 ppc64el 0.10.6-2build1 [234 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcurl3t64-gnutls ppc64el 8.5.0-2ubuntu9 [419 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libcurl4-gnutls-dev ppc64el 8.5.0-2ubuntu9 [530 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate-dev ppc64el 1.19-1 [69.7 kB] Get:45 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs2 ppc64el 1.6.0-1 [110 kB] Get:46 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhtscodecs-dev ppc64el 1.6.0-1 [3007 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libssl-dev ppc64el 3.0.13-0ubuntu3 [2666 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg-3.1ubuntu2 [902 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el liblzma-dev ppc64el 5.6.1+really5.4.5-1build1 [207 kB] Preconfiguring packages ... Fetched 29.0 MB in 2s (17.6 MB/s) Selecting previously unselected package libelf1t64:ppc64el. (Reading database ... 15707 files and directories currently installed.) Preparing to unpack .../00-libelf1t64_0.190-1.1build3_ppc64el.deb ... Unpacking libelf1t64:ppc64el (0.190-1.1build3) ... Selecting previously unselected package libicu74:ppc64el. Preparing to unpack .../01-libicu74_74.2-1ubuntu1_ppc64el.deb ... Unpacking libicu74:ppc64el (74.2-1ubuntu1) ... Selecting previously unselected package libxml2:ppc64el. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.3ubuntu3_ppc64el.deb ... Unpacking libxml2:ppc64el (2.9.14+dfsg-1.3ubuntu3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3build1_ppc64el.deb ... Unpacking libmagic-mgc (1:5.45-3build1) ... Selecting previously unselected package libmagic1t64:ppc64el. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3build1_ppc64el.deb ... 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Setting up libpipeline1:ppc64el (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:ppc64el (1.1.0-2build1) ... Setting up libmagic1t64:ppc64el (1:5.45-3build1) ... Setting up libpsl5t64:ppc64el (0.21.2-1.1build1) ... Setting up libnghttp2-14:ppc64el (1.59.0-1build2) ... Setting up libdeflate0:ppc64el (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:ppc64el (0.190-1.1build3) ... Setting up libdw1t64:ppc64el (0.190-1.1build3) ... Setting up libsasl2-modules-db:ppc64el (2.1.28+dfsg1-5ubuntu2) ... Setting up libhtscodecs-dev:ppc64el (1.6.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d.1-2build7) ... Setting up libssl-dev:ppc64el (3.0.13-0ubuntu3) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up libsasl2-2:ppc64el (2.1.28+dfsg1-5ubuntu2) ... Setting up libssh-4:ppc64el (0.10.6-2build1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:ppc64el (5.6.1+really5.4.5-1build1) ... Setting up libicu74:ppc64el (74.2-1ubuntu1) ... Setting up zlib1g-dev:ppc64el (1:1.3.dfsg-3.1ubuntu2) ... Setting up dwz (0.15-1build5) ... Setting up libuchardet0:ppc64el (0.0.8-1) ... Setting up debugedit (1:5.0-5build1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libdeflate-dev:ppc64el (1.19-1) ... Setting up libxml2:ppc64el (2.9.14+dfsg-1.3ubuntu3) ... Setting up libldap2:ppc64el (2.6.7+dfsg-1~exp1ubuntu7) ... Setting up libbz2-dev:ppc64el (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:ppc64el (8.5.0-2ubuntu9) ... Setting up libcurl4-gnutls-dev:ppc64el (8.5.0-2ubuntu9) ... 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 (ppc64el included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:35 UTC 2024 ppc64el (ppc64le) 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-common_2.42-4ubuntu2 binutils-powerpc64le-linux-gnu_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-powerpc64le-linux-gnu_13.2.0-23ubuntu3 cpp-powerpc64le-linux-gnu_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-powerpc64le-linux-gnu_13.2.0-23ubuntu3 g++-powerpc64le-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-23ubuntu3 gcc-13-base_13.2.0-23ubuntu3 gcc-13-powerpc64le-linux-gnu_13.2.0-23ubuntu3 gcc-14-base_14-20240330-1ubuntu2 gcc-powerpc64le-linux-gnu_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_8.5.0-2ubuntu9 libcurl4-gnutls-dev_8.5.0-2ubuntu9 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 libitm1_14-20240330-1ubuntu2 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~exp1ubuntu7 liblocale-gettext-perl_1.07-6ubuntu5 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_14-20240330-1ubuntu2 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 libperl5.36_5.36.0-9ubuntu1 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 libquadmath0_14-20240330-1ubuntu2 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 libtsan2_14-20240330-1ubuntu2 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-27988873 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27988873 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27988873 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 ppc64el 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/powerpc64le-linux-gnu/htslib' \ --with-external-htscodecs \ --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/powerpc64le-linux-gnu/htslib' ./configure --build=powerpc64le-linux-gnu --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/powerpc64le-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/usr/lib/powerpc64le-linux-gnu/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/powerpc64le-linux-gnu/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... powerpc64le-unknown-linux-gnu checking host system type... powerpc64le-unknown-linux-gnu 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/powerpc64le-linux-gnu make -j4 "CFLAGS=-g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3" PACKAGE_VERSION=1.19 libdir=/usr/lib/powerpc64le-linux-gnu make[2]: Entering directory '/<>' gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kfunc.o kfunc.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o kstring.o kstring.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzf.o bgzf.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o errmod.o errmod.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o faidx.o faidx.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o header.o header.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -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 -Wdate-time -D_FORTIFY_SOURCE=3' \ '-g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_expr.o hts_expr.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o hts_os.o hts_os.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o md5.o md5.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o multipart.o multipart.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o probaln.o probaln.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o realn.o realn.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o regidx.o regidx.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o region.o region.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam.o sam.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o sam_mods.o sam_mods.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf_sweep.o vcf_sweep.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tbx.o tbx.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o textutils.o textutils.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o thread_pool.o thread_pool.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcf.o vcf.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o vcfutils.o vcfutils.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_external.o cram/cram_external.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_index.o cram/cram_index.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_io.o cram/cram_io.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/mFILE.o cram/mFILE.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/powerpc64le-linux-gnu/htslib\" -c -o plugin.o plugin.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kfunc.pico kfunc.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o kstring.pico kstring.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security 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-ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o faidx.pico faidx.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o header.pico header.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile.pico hfile.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts.pico hts.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts_expr.pico hts_expr.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hts_os.pico hts_os.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o md5.pico md5.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o multipart.pico multipart.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o probaln.pico probaln.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o realn.pico realn.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o regidx.pico regidx.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o region.pico region.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam.pico sam.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o sam_mods.pico sam_mods.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcf_sweep.pico vcf_sweep.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o tbx.pico tbx.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o textutils.pico textutils.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o thread_pool.pico thread_pool.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcf.pico vcf.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o vcfutils.pico vcfutils.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_external.pico cram/cram_external.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_index.pico cram/cram_index.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_io.pico cram/cram_io.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/mFILE.pico cram/mFILE.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -DPLUGINPATH=\"/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/powerpc64le-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o annot-tsv.o annot-tsv.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o bgzip.o bgzip.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o htsfile.o htsfile.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o tabix.o tabix.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_libcurl.pico hfile_libcurl.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_gcs.pico hfile_gcs.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3.pico hfile_s3.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -c -o hfile_s3_write.pico hfile_s3_write.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hts_endian.o test/hts_endian.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fieldarith.o test/fieldarith.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/hfile.o test/hfile.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup.o test/pileup.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/pileup_mod.o test/pileup_mod.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/plugins-dlhts.o test/plugins-dlhts.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/sam.o test/sam.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_bgzf.o test/test_bgzf.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_expr.o test/test_expr.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_faidx.o test/test_faidx.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kfunc.o test/test_kfunc.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_kstring.o test/test_kstring.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_mod.o test/test_mod.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_realn.o test/test_realn.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-regidx.o test/test-regidx.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_str2int.o test/test_str2int.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_time_funcs.o test/test_time_funcs.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_view.o test/test_view.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_index.o test/test_index.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-bcf-translate.o test/test-bcf-translate.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o test/test_introspection.o test/test_introspection.c gcc -g -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -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 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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 ln -sf libhts.so libhts.so.3 gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -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 -shared -Wl,-E -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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 -flto=auto -ffat-lto-objects -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/powerpc64le-linux-gnu \ || \ 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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3" PACKAGE_VERSION=1.19 libdir=/usr/lib/powerpc64le-linux-gnu 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/QtZHDcfZfG/index.bam.csi /<>/test/index.sam > /tmp/QtZHDcfZfG/index.bam .. ok test_index: /<>/test/test_index -c /tmp/QtZHDcfZfG/index.bam .. ok test_index: /<>/test/test_view -l 0 -b -m 0 -x /tmp/QtZHDcfZfG/index.bam.bai /<>/test/index.sam > /tmp/QtZHDcfZfG/index.bam .. ok test_index: /<>/test/test_index -b /tmp/QtZHDcfZfG/index.bam .. ok test_index: /<>/test/test_view -l 0 -z -m 14 -x /tmp/QtZHDcfZfG/index.sam.gz.csi /<>/test/index.sam > /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 0 -x /tmp/QtZHDcfZfG/index.sam.gz.bai /<>/test/index.sam > /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 14 -x /tmp/QtZHDcfZfG/index.sam.gz.csi /<>/test/index_dos.sam > /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 0 -x /tmp/QtZHDcfZfG/index.sam.gz.bai /<>/test/index_dos.sam > /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -C -x /tmp/QtZHDcfZfG/index.cram.crai /<>/test/index.sam > /tmp/QtZHDcfZfG/index.cram .. ok test_index: /<>/test/test_index /tmp/QtZHDcfZfG/index.cram .. ok test_index: /<>/test/test_view -l 0 -b -m 14 -x /tmp/QtZHDcfZfG/index.bcf.csi /<>/test/index.vcf > /tmp/QtZHDcfZfG/index.bcf .. ok test_index: /<>/test/test_index -c /tmp/QtZHDcfZfG/index.bcf .. ok test_index: /<>/test/test_view -l 0 -z -m 14 -x /tmp/QtZHDcfZfG/index.vcf.gz.csi /<>/test/index.vcf > /tmp/QtZHDcfZfG/index.vcf.gz .. ok test_index: /<>/test/test_index -c /tmp/QtZHDcfZfG/index.vcf.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 0 -x /tmp/QtZHDcfZfG/index.vcf.gz.tbi /<>/test/index.vcf > /tmp/QtZHDcfZfG/index.vcf.gz .. ok test_index: /<>/test/test_index -t /tmp/QtZHDcfZfG/index.vcf.gz .. ok test_index: /<>/tabix /tmp/QtZHDcfZfG/index.vcf.gz##idx##/tmp/QtZHDcfZfG/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /<>/test/test_view /tmp/QtZHDcfZfG/index2.bam 1:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/QtZHDcfZfG/index2.bam 1:2000000-2000000 .. ok test_index: /<>/test/test_view /tmp/QtZHDcfZfG/index2.bam 2:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/QtZHDcfZfG/index2.bam 2:2000000-2000000 .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/QtZHDcfZfG/index.bam.csi /<>/test/index.sam > /tmp/QtZHDcfZfG/index.bam .. ok test_index: /<>/test/test_index -c /tmp/QtZHDcfZfG/index.bam .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 0 -x /tmp/QtZHDcfZfG/index.bam.bai /<>/test/index.sam > /tmp/QtZHDcfZfG/index.bam .. ok test_index: /<>/test/test_index -b /tmp/QtZHDcfZfG/index.bam .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/QtZHDcfZfG/index.sam.gz.csi /<>/test/index.sam > /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/QtZHDcfZfG/index.sam.gz.bai /<>/test/index.sam > /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/QtZHDcfZfG/index.sam.gz.csi /<>/test/index_dos.sam > /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/QtZHDcfZfG/index.sam.gz.bai /<>/test/index_dos.sam > /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/QtZHDcfZfG/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -C -x /tmp/QtZHDcfZfG/index.cram.crai /<>/test/index.sam > /tmp/QtZHDcfZfG/index.cram .. ok test_index: /<>/test/test_index /tmp/QtZHDcfZfG/index.cram .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/QtZHDcfZfG/index.bcf.csi /<>/test/index.vcf > /tmp/QtZHDcfZfG/index.bcf .. ok test_index: /<>/test/test_index -c /tmp/QtZHDcfZfG/index.bcf .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/QtZHDcfZfG/index.vcf.gz.csi /<>/test/index.vcf > /tmp/QtZHDcfZfG/index.vcf.gz .. ok test_index: /<>/test/test_index -c /tmp/QtZHDcfZfG/index.vcf.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/QtZHDcfZfG/index.vcf.gz.tbi /<>/test/index.vcf > /tmp/QtZHDcfZfG/index.vcf.gz .. ok test_index: /<>/test/test_index -t /tmp/QtZHDcfZfG/index.vcf.gz .. ok test_index: /<>/tabix /tmp/QtZHDcfZfG/index.vcf.gz##idx##/tmp/QtZHDcfZfG/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /<>/test/test_view /tmp/QtZHDcfZfG/index2.bam 1:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/QtZHDcfZfG/index2.bam 1:2000000-2000000 .. ok test_index: /<>/test/test_view /tmp/QtZHDcfZfG/index2.bam 2:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/QtZHDcfZfG/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/QtZHDcfZfG/test-vcf-api.bcf .. ok test_bcf2vcf: /<>/test/test_view /<>/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /<>/test/test-vcf-sweep /tmp/QtZHDcfZfG/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/QtZHDcfZfG -s 74452500 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/QtZHDcfZfG -s 34270147 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/QtZHDcfZfG -s 11108528 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/QtZHDcfZfG -s 42233895 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/QtZHDcfZfG -s 8111117 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/QtZHDcfZfG -s 85644070 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/QtZHDcfZfG -s 49879942 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/QtZHDcfZfG -s 47881429 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/QtZHDcfZfG -s 69081244 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/QtZHDcfZfG -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/QtZHDcfZfG/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/QtZHDcfZfG/no_index_2.out 2> /tmp/QtZHDcfZfG/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/QtZHDcfZfG/no_index_3.out 2> /tmp/QtZHDcfZfG/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/QtZHDcfZfG/no_index_4.out 2> /tmp/QtZHDcfZfG/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /<>/test/test_view -b -p /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf -x /tmp/QtZHDcfZfG/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/QtZHDcfZfG/range_test_1.out.vcf -r '1' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_2.out.vcf -r '1:1-2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_4.out.vcf -r '1:1-1' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_5.out.vcf -r '{1:1}' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/QtZHDcfZfG/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/QtZHDcfZfG/range_test_14.out.vcf -t '1' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_15.out.vcf -t '1:1-2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_17.out.vcf -t '1:1-1' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_18.out.vcf -t '{1:1}' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/QtZHDcfZfG/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/QtZHDcfZfG/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/QtZHDcfZfG/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/QtZHDcfZfG/headernul0.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/QtZHDcfZfG/headernul1.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/QtZHDcfZfG/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-IobSPmmg 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/powerpc64le-linux-gnu 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 -O3 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -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 -Wdate-time -D_FORTIFY_SOURCE=3" PACKAGE_VERSION=1.19 libdir=/usr/lib/powerpc64le-linux-gnu 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/powerpc64le-linux-gnu /<>/debian/tmp/usr/share/man/man1 /<>/debian/tmp/usr/share/man/man5 /<>/debian/tmp/usr/share/man/man7 /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/pkgconfig if test -n "/usr/lib/powerpc64le-linux-gnu/htslib"; then mkdir -p -m 755 /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/htslib; fi install -p -m 644 libhts.so /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/powerpc64le-linux-gnu#g;s#@-PACKAGE_VERSION@#1.19#g' htslib.pc.tmp > /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/pkgconfig/htslib.pc ln -sf libhts.so.1.19 /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so ln -sf libhts.so.1.19 /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so.3 chmod 644 /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/pkgconfig/htslib.pc 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/powerpc64le-linux-gnu/htslib; fi install -p -m 644 htslib/*.h /<>/debian/tmp/usr/include/htslib install -p -m 644 libhts.a /<>/debian/tmp/usr/lib/powerpc64le-linux-gnu/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/powerpc64le-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/powerpc64le-linux-gnu/htslib debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so.3 debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/ 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/powerpc64le-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.a debian/tmp/usr/lib/powerpc64le-linux-gnu/libhts.so debian/libhts-dev/usr/lib/powerpc64le-linux-gnu/ install -m0755 -d debian/libhts-dev/usr/lib/powerpc64le-linux-gnu/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/powerpc64le-linux-gnu/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/powerpc64le-linux-gnu/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/powerpc64le-linux-gnu/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/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/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/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/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 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/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 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/powerpc64le-linux-gnu/libhts.so.3 ln -s libhts.so.1.19 debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.3 rm -f debian/libhts-dev/usr/lib/powerpc64le-linux-gnu/libhts.so ln -s libhts.so.1.19 debian/libhts-dev/usr/lib/powerpc64le-linux-gnu/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/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian 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 gzip -9nf usr/share/doc/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian 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 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/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 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/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/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 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/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix/usr/share/man -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/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 -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 -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/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/libhts3t64/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/libhts3t64/usr/lib/debug/.dwz/powerpc64le-linux-gnu dwz -mdebian/libhts3t64/usr/lib/debug/.dwz/powerpc64le-linux-gnu/libhts3t64.debug -M/usr/lib/debug/.dwz/powerpc64le-linux-gnu/libhts3t64.debug -- debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 install -m0755 -d debian/tabix/usr/lib/debug/.dwz/powerpc64le-linux-gnu dwz -mdebian/tabix/usr/lib/debug/.dwz/powerpc64le-linux-gnu/tabix.debug -M/usr/lib/debug/.dwz/powerpc64le-linux-gnu/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix dwz: debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19: DWARF compression not beneficial - old size 1040173 new size 1049513 objcopy --compress-debug-sections debian/libhts3t64/usr/lib/debug/.dwz/powerpc64le-linux-gnu/libhts3t64.debug chmod 0644 -- debian/libhts3t64/usr/lib/debug/.dwz/powerpc64le-linux-gnu/libhts3t64.debug objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/powerpc64le-linux-gnu/tabix.debug chmod 0644 -- debian/tabix/usr/lib/debug/.dwz/powerpc64le-linux-gnu/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=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 debugedit --build-id --build-id-seed=tabix/1.19\+ds-1.1build3 debian/tabix/usr/bin/htsfile debugedit: debian/tabix/usr/bin/htsfile: Unknown DWARF DW_FORM_0x1f21 fafadd2af165a250629cdd728fe73175d70baa58 install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fa objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fa/fadd2af165a250629cdd728fe73175d70baa58.debug 645090b2b747e050bc23067ccffab56170b95bca install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/64 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/64/5090b2b747e050bc23067ccffab56170b95bca.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fa/fadd2af165a250629cdd728fe73175d70baa58.debug strip --remove-section=.comment --remove-section=.note -o /tmp/vxlrcwCaEX/stripA8Se_9 debian/tabix/usr/bin/htsfile chmod --reference debian/tabix/usr/bin/htsfile /tmp/vxlrcwCaEX/stripA8Se_9 cat '/tmp/vxlrcwCaEX/stripA8Se_9' > 'debian/tabix/usr/bin/htsfile' chmod --reference /tmp/vxlrcwCaEX/stripA8Se_9 debian/tabix/usr/bin/htsfile objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/fa/fadd2af165a250629cdd728fe73175d70baa58.debug debian/tabix/usr/bin/htsfile /tmp/vxlrcwCaEX/objcopyaajMO5 chmod --reference debian/tabix/usr/bin/htsfile /tmp/vxlrcwCaEX/objcopyaajMO5 cat '/tmp/vxlrcwCaEX/objcopyaajMO5' > 'debian/tabix/usr/bin/htsfile' chmod --reference /tmp/vxlrcwCaEX/objcopyaajMO5 debian/tabix/usr/bin/htsfile debugedit --build-id --build-id-seed=tabix/1.19\+ds-1.1build3 debian/tabix/usr/bin/tabix debugedit: debian/tabix/usr/bin/tabix: Unknown DWARF DW_FORM_0x1f20 25ca236e7ecee0339200ed9634f0ac0f3f88cacd chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/64/5090b2b747e050bc23067ccffab56170b95bca.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/KObkGZuAvZ/strip6bNiOa debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 chmod --reference debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 /tmp/KObkGZuAvZ/strip6bNiOa install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/25 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/25/ca236e7ecee0339200ed9634f0ac0f3f88cacd.debug cat '/tmp/KObkGZuAvZ/strip6bNiOa' > 'debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19' chmod --reference /tmp/KObkGZuAvZ/strip6bNiOa debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/64/5090b2b747e050bc23067ccffab56170b95bca.debug debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 /tmp/KObkGZuAvZ/objcopyWHq0XU chmod --reference debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 /tmp/KObkGZuAvZ/objcopyWHq0XU cat '/tmp/KObkGZuAvZ/objcopyWHq0XU' > 'debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19' chmod --reference /tmp/KObkGZuAvZ/objcopyWHq0XU debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so debugedit: debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so: Unknown DWARF DW_FORM_0x1f20 c7e29ce291716a0c8603f0a29cd4957f72ad08ce install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/c7 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/c7/e29ce291716a0c8603f0a29cd4957f72ad08ce.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/c7/e29ce291716a0c8603f0a29cd4957f72ad08ce.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/KObkGZuAvZ/stripXbnMun debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so chmod --reference debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so /tmp/KObkGZuAvZ/stripXbnMun cat '/tmp/KObkGZuAvZ/stripXbnMun' > 'debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so' chmod --reference /tmp/KObkGZuAvZ/stripXbnMun debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/c7/e29ce291716a0c8603f0a29cd4957f72ad08ce.debug debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so /tmp/KObkGZuAvZ/objcopy02dcSr chmod --reference debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so /tmp/KObkGZuAvZ/objcopy02dcSr cat '/tmp/KObkGZuAvZ/objcopy02dcSr' > 'debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so' chmod --reference /tmp/KObkGZuAvZ/objcopy02dcSr debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so debugedit: debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so: Unknown DWARF DW_FORM_0x1f20 f0ded5ac08bd96d57b41c8a718e6c6a334ddcbae install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/f0 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/f0/ded5ac08bd96d57b41c8a718e6c6a334ddcbae.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/f0/ded5ac08bd96d57b41c8a718e6c6a334ddcbae.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/KObkGZuAvZ/stripOVcoCr debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so chmod --reference debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so /tmp/KObkGZuAvZ/stripOVcoCr cat '/tmp/KObkGZuAvZ/stripOVcoCr' > 'debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so' chmod --reference /tmp/KObkGZuAvZ/stripOVcoCr debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/f0/ded5ac08bd96d57b41c8a718e6c6a334ddcbae.debug debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so /tmp/KObkGZuAvZ/objcopy321Ofu chmod --reference debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so /tmp/KObkGZuAvZ/objcopy321Ofu cat '/tmp/KObkGZuAvZ/objcopy321Ofu' > 'debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so' chmod --reference /tmp/KObkGZuAvZ/objcopy321Ofu debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so debugedit: debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so: Unknown DWARF DW_FORM_0x1f21 baff86ec14942bf3a31fc8601a69bdc15c255dea install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/ba objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/ba/ff86ec14942bf3a31fc8601a69bdc15c255dea.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/ba/ff86ec14942bf3a31fc8601a69bdc15c255dea.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/KObkGZuAvZ/stripgGbK1R debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so chmod --reference debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so /tmp/KObkGZuAvZ/stripgGbK1R cat '/tmp/KObkGZuAvZ/stripgGbK1R' > 'debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so' chmod --reference /tmp/KObkGZuAvZ/stripgGbK1R debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/ba/ff86ec14942bf3a31fc8601a69bdc15c255dea.debug debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so /tmp/KObkGZuAvZ/objcopyed2sE5 chmod --reference debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so /tmp/KObkGZuAvZ/objcopyed2sE5 cat '/tmp/KObkGZuAvZ/objcopyed2sE5' > 'debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so' chmod --reference /tmp/KObkGZuAvZ/objcopyed2sE5 debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so debugedit: debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so: Unknown DWARF DW_FORM_0x1f20 698dab10fdb1e8337539ee34c78ff280d9f024e4 install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/69 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/69/8dab10fdb1e8337539ee34c78ff280d9f024e4.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/69/8dab10fdb1e8337539ee34c78ff280d9f024e4.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/KObkGZuAvZ/stripWAGZjj debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so chmod --reference debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so /tmp/KObkGZuAvZ/stripWAGZjj cat '/tmp/KObkGZuAvZ/stripWAGZjj' > 'debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so' chmod --reference /tmp/KObkGZuAvZ/stripWAGZjj debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/69/8dab10fdb1e8337539ee34c78ff280d9f024e4.debug debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so /tmp/KObkGZuAvZ/objcopyokH7og chmod --reference debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so /tmp/KObkGZuAvZ/objcopyokH7og cat '/tmp/KObkGZuAvZ/objcopyokH7og' > 'debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so' chmod --reference /tmp/KObkGZuAvZ/objcopyokH7og debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/libhts3t64/usr/lib/debug/.dwz/powerpc64le-linux-gnu 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/25/ca236e7ecee0339200ed9634f0ac0f3f88cacd.debug strip --remove-section=.comment --remove-section=.note -o /tmp/vxlrcwCaEX/stripmdZDm7 debian/tabix/usr/bin/tabix chmod --reference debian/tabix/usr/bin/tabix /tmp/vxlrcwCaEX/stripmdZDm7 cat '/tmp/vxlrcwCaEX/stripmdZDm7' > 'debian/tabix/usr/bin/tabix' chmod --reference /tmp/vxlrcwCaEX/stripmdZDm7 debian/tabix/usr/bin/tabix objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/25/ca236e7ecee0339200ed9634f0ac0f3f88cacd.debug debian/tabix/usr/bin/tabix /tmp/vxlrcwCaEX/objcopy99A27w chmod --reference debian/tabix/usr/bin/tabix /tmp/vxlrcwCaEX/objcopy99A27w cat '/tmp/vxlrcwCaEX/objcopy99A27w' > 'debian/tabix/usr/bin/tabix' chmod --reference /tmp/vxlrcwCaEX/objcopy99A27w debian/tabix/usr/bin/tabix 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 8af5dfd5af9a26d6fde45acab71d00d55af6d7ea install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8a objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8a/f5dfd5af9a26d6fde45acab71d00d55af6d7ea.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8a/f5dfd5af9a26d6fde45acab71d00d55af6d7ea.debug strip --remove-section=.comment --remove-section=.note -o /tmp/vxlrcwCaEX/stripie0PXY debian/tabix/usr/bin/bgzip chmod --reference debian/tabix/usr/bin/bgzip /tmp/vxlrcwCaEX/stripie0PXY cat '/tmp/vxlrcwCaEX/stripie0PXY' > 'debian/tabix/usr/bin/bgzip' chmod --reference /tmp/vxlrcwCaEX/stripie0PXY debian/tabix/usr/bin/bgzip objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/8a/f5dfd5af9a26d6fde45acab71d00d55af6d7ea.debug debian/tabix/usr/bin/bgzip /tmp/vxlrcwCaEX/objcopyj3iXC_ chmod --reference debian/tabix/usr/bin/bgzip /tmp/vxlrcwCaEX/objcopyj3iXC_ cat '/tmp/vxlrcwCaEX/objcopyj3iXC_' > 'debian/tabix/usr/bin/bgzip' chmod --reference /tmp/vxlrcwCaEX/objcopyj3iXC_ 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/powerpc64le-linux-gnu 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/powerpc64le-linux-gnu/libhts.so.1.19 mv debian/.debhelper/generated/libhts3t64/triggers.new debian/.debhelper/generated/libhts3t64/triggers mv debian/libhts3t64.substvars.new debian/libhts3t64.substvars 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/htsfile debian/tabix/usr/bin/tabix debian/tabix/usr/bin/bgzip install -m0755 -d debian/libhts3t64/DEBIAN dpkg-shlibdeps -Tdebian/libhts3t64.substvars debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so 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=645090b2b747e050bc23067ccffab56170b95bca 698dab10fdb1e8337539ee34c78ff280d9f024e4 baff86ec14942bf3a31fc8601a69bdc15c255dea c7e29ce291716a0c8603f0a29cd4957f72ad08ce f0ded5ac08bd96d57b41c8a718e6c6a334ddcbae" -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=25ca236e7ecee0339200ed9634f0ac0f3f88cacd 8af5dfd5af9a26d6fde45acab71d00d55af6d7ea fafadd2af165a250629cdd728fe73175d70baa58" -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -Pdebian/libhts3t64 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/libhts3t64/DEBIAN/control chmod 0644 -- debian/tabix/DEBIAN/control dh_md5sums -a install -m0755 -d debian/libhts3t64/DEBIAN install -m0755 -d debian/libhts-dev/DEBIAN cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums install -m0755 -d debian/tabix/DEBIAN cd debian/libhts3t64 >/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 chmod 0644 -- debian/libhts3t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN cd debian/.debhelper/libhts3t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/tabix/DEBIAN/md5sums install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/libhts-dev/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/libhts3t64/DEBIAN/control, package libhts3t64, directory debian/libhts3t64 pkgstripfiles: processing control file: debian/libhts-dev/DEBIAN/control, package libhts-dev, directory debian/libhts-dev .. removing usr/share/doc/libhts3t64/changelog.gz .. removing usr/share/doc/libhts-dev/changelog.gz INFO: pkgstripfiles: waiting for lock (libhts-dev) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package libhts3t64 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libhts3t64' in '../libhts3t64_1.19+ds-1.1build3_ppc64el.deb'. 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_ppc64el.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/libhts3t64/dbgsym-root debian/.debhelper/scratch-space/build-libhts3t64 Renaming tabix-dbgsym_1.19+ds-1.1build3_ppc64el.deb to tabix-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb mv debian/.debhelper/scratch-space/build-tabix/tabix-dbgsym_1.19\+ds-1.1build3_ppc64el.deb ../tabix-dbgsym_1.19\+ds-1.1build3_ppc64el.ddeb INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libhts3t64-dbgsym (in debian/.debhelper/libhts3t64/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com 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_ppc64el.deb'. 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. dpkg-deb: building package 'libhts-dev' in '../libhts-dev_1.19+ds-1.1build3_ppc64el.deb'. Renaming libhts3t64-dbgsym_1.19+ds-1.1build3_ppc64el.deb to libhts3t64-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb mv debian/.debhelper/scratch-space/build-libhts3t64/libhts3t64-dbgsym_1.19\+ds-1.1build3_ppc64el.deb ../libhts3t64-dbgsym_1.19\+ds-1.1build3_ppc64el.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_ppc64el.deb'. dpkg-genbuildinfo --build=any -O../htslib_1.19+ds-1.1build3_ppc64el.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../htslib_1.19+ds-1.1build3_ppc64el.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 2024-03-31T23:17:21Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ htslib_1.19+ds-1.1build3_ppc64el.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: ppc64el 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: fb847057167fca5a4eeaa4fc959a866b48079289 7859 htslib_1.19+ds-1.1build3_ppc64el.buildinfo 399fbe42e278c5e091aa7907b216579994dddfe4 6342708 libhts-dev_1.19+ds-1.1build3_ppc64el.deb 1a223e2fe34f801361d72a55e0259c58d2b1de35 1458906 libhts3t64-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb d551fbbc99b848450ca9adbc30c389eee2b68f41 568876 libhts3t64_1.19+ds-1.1build3_ppc64el.deb c31281052910f9967549f357b72dde7cb8654171 3291196 tabix-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb 8244866a3d181d4a33acdb23a3a7e0c08661c2dd 709776 tabix_1.19+ds-1.1build3_ppc64el.deb Checksums-Sha256: 655f17ebb65f40aa5d3e89693ad34bdebaad7d907feccda67e671d1ce420934b 7859 htslib_1.19+ds-1.1build3_ppc64el.buildinfo c7bc99233a2f3b200a5f845babac7d2a8037b6754ba2bc26eee5a9ed7a45462f 6342708 libhts-dev_1.19+ds-1.1build3_ppc64el.deb 7ad2045adb02814be302fd626020315c78f2ca951ffadcd06c95944c92d92c5d 1458906 libhts3t64-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb 6c9b1c2b039124b3fd020659ced390a0949e3bfb985488beb05e95c7191fa603 568876 libhts3t64_1.19+ds-1.1build3_ppc64el.deb 8c32b3aa7c3676bd7ba61bc958a66626567af6cb22c39e3765e92950b6409267 3291196 tabix-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb 44384ece93e4459d51d0c537d4f9874bee684791054e69bd2e7fa571be844c3a 709776 tabix_1.19+ds-1.1build3_ppc64el.deb Files: 48070576a452ef0e828341b9870eea44 7859 science optional htslib_1.19+ds-1.1build3_ppc64el.buildinfo a8dc4ad6c7b95f434a8eef0794b0a19d 6342708 libdevel optional libhts-dev_1.19+ds-1.1build3_ppc64el.deb 5936fe5b7198a5d37008892e4bf41803 1458906 debug optional libhts3t64-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb 6072c27d582351ac92a9babb80ab0ff7 568876 libs optional libhts3t64_1.19+ds-1.1build3_ppc64el.deb 02f1ffc884a9702d3ec06ac3e8b33a2e 3291196 debug optional tabix-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb 5ca92c2421050f0bc309a5831ed49b93 709776 science optional tabix_1.19+ds-1.1build3_ppc64el.deb Original-Maintainer: Debian Med Packaging Team /<>/htslib_1.19+ds-1.1build3_ppc64el.changes.new could not be renamed to /<>/htslib_1.19+ds-1.1build3_ppc64el.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: htslib Binary: libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: ppc64el Version: 1.19+ds-1.1build3 Checksums-Md5: a8dc4ad6c7b95f434a8eef0794b0a19d 6342708 libhts-dev_1.19+ds-1.1build3_ppc64el.deb 5936fe5b7198a5d37008892e4bf41803 1458906 libhts3t64-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb 6072c27d582351ac92a9babb80ab0ff7 568876 libhts3t64_1.19+ds-1.1build3_ppc64el.deb 02f1ffc884a9702d3ec06ac3e8b33a2e 3291196 tabix-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb 5ca92c2421050f0bc309a5831ed49b93 709776 tabix_1.19+ds-1.1build3_ppc64el.deb Checksums-Sha1: 399fbe42e278c5e091aa7907b216579994dddfe4 6342708 libhts-dev_1.19+ds-1.1build3_ppc64el.deb 1a223e2fe34f801361d72a55e0259c58d2b1de35 1458906 libhts3t64-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb d551fbbc99b848450ca9adbc30c389eee2b68f41 568876 libhts3t64_1.19+ds-1.1build3_ppc64el.deb c31281052910f9967549f357b72dde7cb8654171 3291196 tabix-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb 8244866a3d181d4a33acdb23a3a7e0c08661c2dd 709776 tabix_1.19+ds-1.1build3_ppc64el.deb Checksums-Sha256: c7bc99233a2f3b200a5f845babac7d2a8037b6754ba2bc26eee5a9ed7a45462f 6342708 libhts-dev_1.19+ds-1.1build3_ppc64el.deb 7ad2045adb02814be302fd626020315c78f2ca951ffadcd06c95944c92d92c5d 1458906 libhts3t64-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb 6c9b1c2b039124b3fd020659ced390a0949e3bfb985488beb05e95c7191fa603 568876 libhts3t64_1.19+ds-1.1build3_ppc64el.deb 8c32b3aa7c3676bd7ba61bc958a66626567af6cb22c39e3765e92950b6409267 3291196 tabix-dbgsym_1.19+ds-1.1build3_ppc64el.ddeb 44384ece93e4459d51d0c537d4f9874bee684791054e69bd2e7fa571be844c3a 709776 tabix_1.19+ds-1.1build3_ppc64el.deb Build-Origin: Ubuntu Build-Architecture: ppc64el Build-Date: Sun, 31 Mar 2024 23:17:21 +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-common (= 2.42-4ubuntu2), binutils-powerpc64le-linux-gnu (= 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-powerpc64le-linux-gnu (= 13.2.0-23ubuntu3), cpp-powerpc64le-linux-gnu (= 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-powerpc64le-linux-gnu (= 13.2.0-23ubuntu3), g++-powerpc64le-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-23ubuntu3), gcc-13-base (= 13.2.0-23ubuntu3), gcc-13-powerpc64le-linux-gnu (= 13.2.0-23ubuntu3), gcc-14-base (= 14-20240330-1ubuntu2), gcc-powerpc64le-linux-gnu (= 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 (= 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), libctf-nobfd0 (= 2.42-4ubuntu2), libctf0 (= 2.42-4ubuntu2), libcurl3t64-gnutls (= 8.5.0-2ubuntu9), libcurl4-gnutls-dev (= 8.5.0-2ubuntu9), libdb5.3t64 (= 5.3.28+dfsg2-6build1), libdebconfclient0 (= 0.271ubuntu3), libdebhelper-perl (= 13.14.1ubuntu5), libdeflate-dev (= 1.19-1), libdeflate0 (= 1.19-1), libdpkg-perl (= 1.22.6ubuntu6), libdw1t64 (= 0.190-1.1build3), libelf1t64 (= 0.190-1.1build3), 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-error0 (= 1.47-3build1), 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), libisl23 (= 0.26-3), libitm1 (= 14-20240330-1ubuntu2), libjansson4 (= 2.14-2build2), libk5crypto3 (= 1.20.1-6ubuntu2), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.20.1-6ubuntu2), libkrb5support0 (= 1.20.1-6ubuntu2), libldap2 (= 2.6.7+dfsg-1~exp1ubuntu7), liblsan0 (= 14-20240330-1ubuntu2), 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), libnettle8t64 (= 3.9.1-2.2build1), libnghttp2-14 (= 1.59.0-1build2), 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), libpsl5t64 (= 0.21.2-1.1build1), libquadmath0 (= 14-20240330-1ubuntu2), 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), libsframe1 (= 2.42-4ubuntu2), libsmartcols1 (= 2.39.3-9ubuntu3), 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), libsystemd0 (= 255.4-1ubuntu5), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20240113-1ubuntu1), libtool (= 2.4.7-7), libtsan2 (= 14-20240330-1ubuntu2), libubsan1 (= 14-20240330-1ubuntu2), libuchardet0 (= 0.0.8-1), libudev1 (= 255.4-1ubuntu5), libunistring5 (= 1.1-2), libuuid1 (= 2.39.3-9ubuntu3), libxml2 (= 2.9.14+dfsg-1.3ubuntu3), libzstd1 (= 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_ppc64el.deb ---------------------------------------- new Debian package, version 2.0. size 6342708 bytes: control archive=1917 bytes. 1314 bytes, 28 lines control 2206 bytes, 34 lines md5sums Package: libhts-dev Source: htslib Version: 1.19+ds-1.1build3 Architecture: ppc64el Maintainer: Ubuntu Developers Installed-Size: 13447 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/powerpc64le-linux-gnu/ -rw-r--r-- root/root 13243402 2024-03-31 18:25 ./usr/lib/powerpc64le-linux-gnu/libhts.a lrwxrwxrwx root/root 0 2024-03-31 18:25 ./usr/lib/powerpc64le-linux-gnu/libhts.so -> libhts.so.1.19 drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/lib/powerpc64le-linux-gnu/pkgconfig/ -rw-r--r-- root/root 788 2024-03-31 18:25 ./usr/lib/powerpc64le-linux-gnu/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_ppc64el.deb ---------------------------------------- new Debian package, version 2.0. size 568876 bytes: control archive=6142 bytes. 1401 bytes, 25 lines control 907 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: ppc64el Maintainer: Ubuntu Developers Installed-Size: 1655 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 Provides: libhts3 (= 1.19+ds-1.1build3) 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/powerpc64le-linux-gnu/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/lib/powerpc64le-linux-gnu/htslib/ -rw-r--r-- root/root 67592 2024-03-31 18:25 ./usr/lib/powerpc64le-linux-gnu/htslib/hfile_gcs.so -rw-r--r-- root/root 67592 2024-03-31 18:25 ./usr/lib/powerpc64le-linux-gnu/htslib/hfile_libcurl.so -rw-r--r-- root/root 67592 2024-03-31 18:25 ./usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3.so -rw-r--r-- root/root 67592 2024-03-31 18:25 ./usr/lib/powerpc64le-linux-gnu/htslib/hfile_s3_write.so -rw-r--r-- root/root 1312976 2024-03-31 18:25 ./usr/lib/powerpc64le-linux-gnu/libhts.so.1.19 lrwxrwxrwx root/root 0 2024-03-31 18:25 ./usr/lib/powerpc64le-linux-gnu/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_ppc64el.deb ----------------------------------- new Debian package, version 2.0. size 709776 bytes: control archive=1059 bytes. 1074 bytes, 21 lines control 478 bytes, 8 lines md5sums Package: tabix Source: htslib Version: 1.19+ds-1.1build3 Architecture: ppc64el Maintainer: Ubuntu Developers Installed-Size: 3528 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 1050992 2024-03-31 18:25 ./usr/bin/bgzip -rwxr-xr-x root/root 1247680 2024-03-31 18:25 ./usr/bin/htsfile -rwxr-xr-x root/root 1247680 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: ppc64el Build Type: any Build-Space: 128476 Build-Time: 309 Distribution: noble-proposed Host Architecture: ppc64el Install-Time: 6 Job: htslib_1.19+ds-1.1build3.dsc Machine Architecture: ppc64el Package: htslib Package-Time: 317 Source-Version: 1.19+ds-1.1build3 Space: 128476 Status: successful Version: 1.19+ds-1.1build3 -------------------------------------------------------------------------------- Finished at 2024-03-31T23:17:21Z Build needed 00:05:17, 128476k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=ppc64el PACKAGEBUILD-27988873 Scanning for processes to kill in build PACKAGEBUILD-27988873