https://launchpad.net/ubuntu/+source/htslib/1.19+ds-1.1build3/+build/27988875 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-006 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:49 UTC 2024 s390x 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 21:42:13 ntpdate[1899]: adjust time server 10.211.37.1 offset 0.001004 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27988875 --image-type chroot /home/buildd/filecache-default/c23f799bb684944311373fdcead5a58221fa6ef7 Creating target for build PACKAGEBUILD-27988875 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27988875 Starting target for build PACKAGEBUILD-27988875 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27988875 '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-27988875 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27988875 Updating target for build PACKAGEBUILD-27988875 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 s390x Packages [1357 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x Packages [14.4 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6118 kB] Get:9 http://ftpmaster.internal/ubuntu noble-updates/main s390x Packages [675 kB] Get:10 http://ftpmaster.internal/ubuntu noble-updates/main Translation-en [242 kB] Get:11 http://ftpmaster.internal/ubuntu noble-updates/universe s390x Packages [4414 kB] Get:12 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [1693 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [508 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [200 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [1554 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [832 kB] Fetched 33.1 MB in 19s (1708 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-s390x-linux-gnu cpp-s390x-linux-gnu g++-13-s390x-linux-gnu g++-s390x-linux-gnu gcc-13-s390x-linux-gnu gcc-14-base gcc-s390x-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-s390x-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 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 154 upgraded, 23 newly installed, 14 to remove and 1 not upgraded. Need to get 105 MB of archives. After this operation, 76.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnsl-dev s390x 1.3.0-3build3 [73.1 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-4 [135 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc6-dev s390x 2.39-0ubuntu8 [1629 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc-dev-bin s390x 2.39-0ubuntu8 [20.2 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc-dev s390x 1.3.4+ds-1.1build1 [197 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x libnss-nisplus s390x 1.3-5 [23.6 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtirpc3t64 s390x 1.3.4+ds-1.1build1 [85.9 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgssapi-krb5-2 s390x 1.20.1-6ubuntu2 [149 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkrb5-3 s390x 1.20.1-6ubuntu2 [360 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libk5crypto3 s390x 1.20.1-6ubuntu2 [90.3 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkrb5support0 s390x 1.20.1-6ubuntu2 [34.7 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libacl1 s390x 2.3.2-1 [18.0 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libapparmor1 s390x 4.0.0-beta3-0ubuntu3 [50.8 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libblkid1 s390x 2.39.3-9ubuntu3 [128 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libcap2 s390x 1:2.66-5ubuntu1 [31.7 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt1 s390x 1:4.4.36-4 [102 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error-l10n all 1.47-3build1 [8024 B] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error0 s390x 1.47-3build1 [75.6 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libgcrypt20 s390x 1.10.3-2 [499 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblzma5 s390x 5.6.1+really5.4.5-1build1 [135 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libzstd1 s390x 1.5.5+dfsg2-2 [336 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libkmod2 s390x 31+20240202-2ubuntu5 [56.3 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-8-0 s390x 10.42-4ubuntu1 [243 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libselinux1 s390x 3.5-2ubuntu2 [84.8 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmount1 s390x 2.39.3-9ubuntu3 [138 kB] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-modules-5.38 all 5.38.2-3.2build1 [3110 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-6build1 [763 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm6t64 s390x 1.23-5.1build1 [36.5 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgdbm-compat4t64 s390x 1.23-5.1build1 [6890 B] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libperl5.38t64 s390x 5.38.2-3.2build1 [5008 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl s390x 5.38.2-3.2build1 [231 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main s390x perl-base s390x 5.38.2-3.2build1 [1968 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblocale-gettext-perl s390x 1.07-6ubuntu5 [15.8 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtext-iconv-perl s390x 1.7-8build3 [13.8 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libtext-charwidth-perl s390x 0.04-11build3 [9518 B] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc6 s390x 2.39-0ubuntu8 [2847 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libc-bin s390x 2.39-0ubuntu8 [654 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu3 [1009 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libsystemd-shared s390x 255.4-1ubuntu5 [2131 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcryptsetup12 s390x 2:2.7.0-1ubuntu3 [264 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu3 [1675 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-dev all 255.4-1ubuntu6 [104 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main s390x systemd-sysv s390x 255.4-1ubuntu5 [11.9 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main s390x systemd s390x 255.4-1ubuntu5 [3533 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main s390x libsystemd0 s390x 255.4-1ubuntu5 [443 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-modules-bin s390x 1.5.3-5ubuntu4 [57.2 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-modules s390x 1.5.3-5ubuntu4 [289 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnettle8t64 s390x 3.9.1-2.2build1 [210 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libhogweed6t64 s390x 3.9.1-2.2build1 [204 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main s390x libp11-kit0 s390x 0.25.3-4ubuntu1 [318 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main s390x libunistring5 s390x 1.1-2 [544 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgnutls30t64 s390x 3.8.3-1.1ubuntu3 [944 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libapt-pkg6.0t64 s390x 2.7.14 [1014 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bzip2 s390x 1.0.8-5.1 [35.5 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libbz2-1.0 s390x 1.0.8-5.1 [40.0 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gcc-14-base s390x 14-20240330-1ubuntu2 [47.4 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgcc-s1 s390x 14-20240330-1ubuntu2 [35.9 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libstdc++6 s390x 14-20240330-1ubuntu2 [905 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main s390x libudev1 s390x 255.4-1ubuntu5 [178 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main s390x libxxhash0 s390x 0.8.2-2 [23.6 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main s390x zlib1g s390x 1:1.3.dfsg-3.1ubuntu2 [75.9 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main s390x libffi8 s390x 3.4.6-1 [23.0 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main s390x libidn2-0 s390x 2.3.7-2 [67.2 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdebconfclient0 s390x 0.271ubuntu3 [11.4 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main s390x base-passwd s390x 3.6.3 [51.1 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsqlite3-0 s390x 3.45.1-1ubuntu2 [747 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg s390x 2.4.4-2ubuntu16 [589 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libreadline8t64 s390x 8.2-4build1 [171 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main s390x readline-common all 8.2-4build1 [56.5 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main s390x libncursesw6 s390x 6.4+20240113-1ubuntu1 [161 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main s390x libtinfo6 s390x 6.4+20240113-1ubuntu1 [117 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpg-agent s390x 2.4.4-2ubuntu16 [240 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgconf s390x 2.4.4-2ubuntu16 [111 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main s390x pinentry-curses s390x 1.2.1-3ubuntu4 [37.6 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main s390x init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnpth0t64 s390x 1.6-3.1build1 [8204 B] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gpgv s390x 2.4.4-2ubuntu16 [165 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libseccomp2 s390x 2.5.5-1ubuntu3 [53.4 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main s390x apt-utils s390x 2.7.14 [214 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main s390x apt s390x 2.7.14 [1390 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main s390x debconf-i18n all 1.5.86 [205 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main s390x debconf all 1.5.86 [124 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam0g s390x 1.5.3-5ubuntu4 [69.7 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main s390x libargon2-1 s390x 0~20190702+dfsg-4 [53.1 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdevmapper1.02.1 s390x 2:1.02.185-3ubuntu3 [142 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libuuid1 s390x 2.39.3-9ubuntu3 [35.8 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libfdisk1 s390x 2.39.3-9ubuntu3 [151 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main s390x mount s390x 2.39.3-9ubuntu3 [119 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcom-err2 s390x 1.47.0-2.4~exp1ubuntu3 [22.9 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main s390x libkeyutils1 s390x 1.6.3-3 [9448 B] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnsl2 s390x 1.3.0-3build3 [44.1 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main s390x linux-libc-dev s390x 6.8.0-20.20 [1592 kB] Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main s390x base-files s390x 13ubuntu9 [73.7 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main s390x debianutils s390x 5.17build1 [90.2 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bash s390x 5.2.21-2ubuntu4 [845 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdutils s390x 1:2.39.3-9ubuntu3 [96.3 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main s390x coreutils s390x 9.4-3ubuntu5 [1482 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main s390x tar s390x 1.35+dfsg-3 [269 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg s390x 1.22.6ubuntu6 [1278 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dash s390x 0.5.12-6ubuntu5 [95.0 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main s390x diffutils s390x 1:3.10-1 [187 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main s390x grep s390x 3.11-4 [189 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main s390x gzip s390x 1.12-1ubuntu2 [106 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main s390x hostname s390x 3.23+nmu2ubuntu1 [11.1 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main s390x login s390x 1:4.13+dfsg1-4ubuntu1 [202 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-bin s390x 6.4+20240113-1ubuntu1 [198 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main s390x sed s390x 4.9-2 [207 kB] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main s390x util-linux s390x 2.39.3-9ubuntu3 [1142 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main s390x sysvinit-utils s390x 3.08-6ubuntu2 [34.7 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main s390x logsave s390x 1.47.0-2.4~exp1ubuntu3 [22.6 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libext2fs2t64 s390x 1.47.0-2.4~exp1ubuntu3 [234 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main s390x e2fsprogs s390x 1.47.0-2.4~exp1ubuntu3 [615 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main s390x optipng s390x 0.7.8+ds-1build2 [114 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpng16-16t64 s390x 1.6.43-5build1 [200 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main s390x init s390x 1.66ubuntu1 [6188 B] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsmartcols1 s390x 2.39.3-9ubuntu3 [68.1 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main s390x uuid-runtime s390x 2.39.3-9ubuntu3 [33.4 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main s390x libattr1 s390x 1:2.5.2-1 [11.7 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main s390x libaudit-common all 1:3.1.2-2.1 [5674 B] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcap-ng0 s390x 0.8.4-2build2 [15.8 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main s390x libmd0 s390x 1.1.0-2 [24.7 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage-common all 3.5-1build4 [10.1 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main s390x libsepol2 s390x 3.5-2 [308 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage2 s390x 3.5-1build4 [96.7 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main s390x passwd s390x 1:4.13+dfsg1-4ubuntu1 [857 kB] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libproc2-0 s390x 2:4.0.4-4ubuntu3 [59.8 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libss2 s390x 1.47.0-2.4~exp1ubuntu3 [17.2 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main s390x mawk s390x 1.3.4.20240123-1 [133 kB] Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main s390x procps s390x 2:4.0.4-4ubuntu3 [724 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main s390x sensible-utils all 0.0.22 [22.5 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main s390x ca-certificates all 20240203 [159 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main s390x krb5-locales all 1.20.1-6ubuntu1 [13.8 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main s390x tzdata all 2024a-1ubuntu1 [273 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main s390x bash-completion all 1:2.11-8 [180 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main s390x bsdextrautils s390x 2.39.3-9ubuntu3 [76.4 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgpm2 s390x 1.20.7-11 [14.7 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main s390x libip4tc2 s390x 1.8.10-3ubuntu1 [24.2 kB] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libjansson4 s390x 2.14-2build2 [33.2 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main s390x psmisc s390x 23.7-1build1 [178 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main s390x xz-utils s390x 5.6.1+really5.4.5-1build1 [269 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main s390x libctf0 s390x 2.42-4ubuntu2 [98.4 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main s390x libctf-nobfd0 s390x 2.42-4ubuntu2 [100 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main s390x binutils-s390x-linux-gnu s390x 2.42-4ubuntu2 [2270 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main s390x libbinutils s390x 2.42-4ubuntu2 [479 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main s390x binutils s390x 2.42-4ubuntu2 [3042 B] Get:150 http://ftpmaster.internal/ubuntu noble/main s390x binutils-common s390x 2.42-4ubuntu2 [217 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main s390x libsframe1 s390x 2.42-4ubuntu2 [14.2 kB] Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libubsan1 s390x 14-20240330-1ubuntu2 [1186 kB] Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgomp1 s390x 14-20240330-1ubuntu2 [151 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libitm1 s390x 14-20240330-1ubuntu2 [31.1 kB] Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libatomic1 s390x 14-20240330-1ubuntu2 [9386 B] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libasan8 s390x 14-20240330-1ubuntu2 [2994 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main s390x g++-13 s390x 13.2.0-23ubuntu3 [14.5 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gcc-13 s390x 13.2.0-23ubuntu3 [469 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libstdc++-13-dev s390x 13.2.0-23ubuntu3 [2494 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libgcc-13-dev s390x 13.2.0-23ubuntu3 [1003 kB] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcc1-0 s390x 14-20240330-1ubuntu2 [49.8 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main s390x cpp-13 s390x 13.2.0-23ubuntu3 [1026 B] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gcc-13-base s390x 13.2.0-23ubuntu3 [48.6 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main s390x gcc-13-s390x-linux-gnu s390x 13.2.0-23ubuntu3 [19.1 MB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main s390x g++-13-s390x-linux-gnu s390x 13.2.0-23ubuntu3 [11.3 MB] Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main s390x cpp-13-s390x-linux-gnu s390x 13.2.0-23ubuntu3 [9936 kB] Get:167 http://ftpmaster.internal/ubuntu noble/main s390x g++ s390x 4:13.2.0-7ubuntu1 [1096 B] Get:168 http://ftpmaster.internal/ubuntu noble/main s390x gcc s390x 4:13.2.0-7ubuntu1 [5014 B] Get:169 http://ftpmaster.internal/ubuntu noble/main s390x cpp s390x 4:13.2.0-7ubuntu1 [22.4 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main s390x cpp-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [5308 B] Get:171 http://ftpmaster.internal/ubuntu noble/main s390x gcc-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1208 B] Get:172 http://ftpmaster.internal/ubuntu noble/main s390x g++-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [956 B] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main s390x dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main s390x lto-disabled-list all 47 [12.4 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main s390x libfakeroot s390x 1.33-1 [31.9 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main s390x fakeroot s390x 1.33-1 [67.5 kB] Preconfiguring packages ... Fetched 105 MB in 9s (11.9 MB/s) (Reading database ... 13395 files and directories currently installed.) Preparing to unpack .../0-libnsl-dev_1.3.0-3build3_s390x.deb ... Unpacking libnsl-dev:s390x (1.3.0-3build3) over (1.3.0-2build2) ... Preparing to unpack .../1-libcrypt-dev_1%3a4.4.36-4_s390x.deb ... Unpacking libcrypt-dev:s390x (1:4.4.36-4) over (1:4.4.36-2) ... Preparing to unpack .../2-libc6-dev_2.39-0ubuntu8_s390x.deb ... Unpacking libc6-dev:s390x (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Preparing to unpack .../3-libc-dev-bin_2.39-0ubuntu8_s390x.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_s390x.deb ... Unpacking libtirpc-dev:s390x (1.3.4+ds-1.1build1) over (1.3.3+ds-1) ... Preparing to unpack .../6-libnss-nisplus_1.3-5_s390x.deb ... Unpacking libnss-nisplus:s390x (1.3-5) over (1.3-0ubuntu6) ... dpkg: libtirpc3:s390x: dependency problems, but removing anyway as you requested: libnsl2:s390x depends on libtirpc3 (>= 1.0.2). (Reading database ... 13398 files and directories currently installed.) Removing libtirpc3:s390x (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3t64:s390x. (Reading database ... 13392 files and directories currently installed.) Preparing to unpack .../0-libtirpc3t64_1.3.4+ds-1.1build1_s390x.deb ... Adding 'diversion of /lib/s390x-linux-gnu/libtirpc.so.3 to /lib/s390x-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/s390x-linux-gnu/libtirpc.so.3.0.0 to /lib/s390x-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:s390x (1.3.4+ds-1.1build1) ... Preparing to unpack .../1-libgssapi-krb5-2_1.20.1-6ubuntu2_s390x.deb ... Unpacking libgssapi-krb5-2:s390x (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ... Preparing to unpack .../2-libkrb5-3_1.20.1-6ubuntu2_s390x.deb ... Unpacking libkrb5-3:s390x (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ... Preparing to unpack .../3-libk5crypto3_1.20.1-6ubuntu2_s390x.deb ... Unpacking libk5crypto3:s390x (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ... Preparing to unpack .../4-libkrb5support0_1.20.1-6ubuntu2_s390x.deb ... Unpacking libkrb5support0:s390x (1.20.1-6ubuntu2) over (1.20.1-3ubuntu1) ... Preparing to unpack .../5-libacl1_2.3.2-1_s390x.deb ... Unpacking libacl1:s390x (2.3.2-1) over (2.3.1-3) ... Setting up libacl1:s390x (2.3.2-1) ... (Reading database ... 13403 files and directories currently installed.) Preparing to unpack .../libapparmor1_4.0.0-beta3-0ubuntu3_s390x.deb ... Unpacking libapparmor1:s390x (4.0.0-beta3-0ubuntu3) over (4.0.0~alpha2-0ubuntu5) ... Preparing to unpack .../libblkid1_2.39.3-9ubuntu3_s390x.deb ... Unpacking libblkid1:s390x (2.39.3-9ubuntu3) over (2.39.1-4ubuntu2) ... Setting up libblkid1:s390x (2.39.3-9ubuntu3) ... (Reading database ... 13403 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-5ubuntu1_s390x.deb ... Unpacking libcap2:s390x (1:2.66-5ubuntu1) over (1:2.66-4ubuntu1) ... Setting up libcap2:s390x (1:2.66-5ubuntu1) ... (Reading database ... 13403 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-4_s390x.deb ... Unpacking libcrypt1:s390x (1:4.4.36-4) over (1:4.4.36-2) ... Setting up libcrypt1:s390x (1:4.4.36-4) ... (Reading database ... 13403 files and directories currently installed.) Preparing to unpack .../libgpg-error-l10n_1.47-3build1_all.deb ... Unpacking libgpg-error-l10n (1.47-3build1) over (1.47-2) ... Preparing to unpack .../libgpg-error0_1.47-3build1_s390x.deb ... Unpacking libgpg-error0:s390x (1.47-3build1) over (1.47-2) ... Setting up libgpg-error0:s390x (1.47-3build1) ... (Reading database ... 13403 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.3-2_s390x.deb ... Unpacking libgcrypt20:s390x (1.10.3-2) over (1.10.2-3ubuntu1) ... Setting up libgcrypt20:s390x (1.10.3-2) ... (Reading database ... 13403 files and directories currently installed.) Preparing to unpack .../liblzma5_5.6.1+really5.4.5-1build1_s390x.deb ... Unpacking liblzma5:s390x (5.6.1+really5.4.5-1build1) over (5.4.1-0.2) ... Setting up liblzma5:s390x (5.6.1+really5.4.5-1build1) ... (Reading database ... 13403 files and directories currently installed.) Preparing to unpack .../libzstd1_1.5.5+dfsg2-2_s390x.deb ... Unpacking libzstd1:s390x (1.5.5+dfsg2-2) over (1.5.5+dfsg2-1ubuntu2) ... Setting up libzstd1:s390x (1.5.5+dfsg2-2) ... (Reading database ... 13403 files and directories currently installed.) Preparing to unpack .../libkmod2_31+20240202-2ubuntu5_s390x.deb ... Unpacking libkmod2:s390x (31+20240202-2ubuntu5) over (30+20230519-1ubuntu3) ... Preparing to unpack .../libpcre2-8-0_10.42-4ubuntu1_s390x.deb ... Unpacking libpcre2-8-0:s390x (10.42-4ubuntu1) over (10.42-4) ... Setting up libpcre2-8-0:s390x (10.42-4ubuntu1) ... (Reading database ... 13403 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-2ubuntu2_s390x.deb ... Unpacking libselinux1:s390x (3.5-2ubuntu2) over (3.5-1) ... Setting up libselinux1:s390x (3.5-2ubuntu2) ... (Reading database ... 13404 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.3-9ubuntu3_s390x.deb ... Unpacking libmount1:s390x (2.39.3-9ubuntu3) over (2.39.1-4ubuntu2) ... Setting up libmount1:s390x (2.39.3-9ubuntu3) ... (Reading database ... 13404 files and directories currently installed.) Preparing to unpack .../perl_5.38.2-3.2build1_s390x.deb ... Unpacking perl (5.38.2-3.2build1) over (5.36.0-9ubuntu1) ... 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:s390x: dependency problems, but removing anyway as you requested: libperl5.36:s390x depends on libdb5.3. libpam-modules:s390x depends on libdb5.3. apt-utils depends on libdb5.3. (Reading database ... 14816 files and directories currently installed.) Removing libdb5.3:s390x (5.3.28+dfsg2-2) ... Selecting previously unselected package libdb5.3t64:s390x. (Reading database ... 14810 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-6build1_s390x.deb ... Unpacking libdb5.3t64:s390x (5.3.28+dfsg2-6build1) ... dpkg: libgdbm6:s390x: dependency problems, but removing anyway as you requested: libperl5.36:s390x depends on libgdbm6 (>= 1.21). libgdbm-compat4:s390x depends on libgdbm6 (>= 1.16). (Reading database ... 14816 files and directories currently installed.) Removing libgdbm6:s390x (1.23-3) ... Selecting previously unselected package libgdbm6t64:s390x. (Reading database ... 14811 files and directories currently installed.) Preparing to unpack .../libgdbm6t64_1.23-5.1build1_s390x.deb ... Unpacking libgdbm6t64:s390x (1.23-5.1build1) ... dpkg: libgdbm-compat4:s390x: dependency problems, but removing anyway as you requested: libperl5.36:s390x depends on libgdbm-compat4 (>= 1.18-3). (Reading database ... 14817 files and directories currently installed.) Removing libgdbm-compat4:s390x (1.23-3) ... Selecting previously unselected package libgdbm-compat4t64:s390x. (Reading database ... 14812 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4t64_1.23-5.1build1_s390x.deb ... Unpacking libgdbm-compat4t64:s390x (1.23-5.1build1) ... Selecting previously unselected package libperl5.38t64:s390x. Preparing to unpack .../libperl5.38t64_5.38.2-3.2build1_s390x.deb ... Unpacking libperl5.38t64:s390x (5.38.2-3.2build1) ... Preparing to unpack .../perl-base_5.38.2-3.2build1_s390x.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 ... 15343 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu5_s390x.deb ... Unpacking liblocale-gettext-perl (1.07-6ubuntu5) over (1.07-6) ... Preparing to unpack .../libtext-iconv-perl_1.7-8build3_s390x.deb ... Unpacking libtext-iconv-perl:s390x (1.7-8build3) over (1.7-8) ... Preparing to unpack .../libtext-charwidth-perl_0.04-11build3_s390x.deb ... Unpacking libtext-charwidth-perl:s390x (0.04-11build3) over (0.04-11) ... Preparing to unpack .../libc6_2.39-0ubuntu8_s390x.deb ... Unpacking libc6:s390x (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Setting up libc6:s390x (2.39-0ubuntu8) ... (Reading database ... 15345 files and directories currently installed.) Preparing to unpack .../libc-bin_2.39-0ubuntu8_s390x.deb ... Unpacking libc-bin (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Setting up libc-bin (2.39-0ubuntu8) ... (Reading database ... 15345 files and directories currently installed.) Preparing to unpack .../openssl_3.0.13-0ubuntu3_s390x.deb ... Unpacking openssl (3.0.13-0ubuntu3) over (3.0.10-1ubuntu2) ... Preparing to unpack .../libsystemd-shared_255.4-1ubuntu5_s390x.deb ... Unpacking libsystemd-shared:s390x (255.4-1ubuntu5) over (253.5-1ubuntu6) ... Preparing to unpack .../libcryptsetup12_2%3a2.7.0-1ubuntu3_s390x.deb ... Unpacking libcryptsetup12:s390x (2:2.7.0-1ubuntu3) over (2:2.6.1-4ubuntu3) ... dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: systemd depends on libssl3 (>= 3.0.0). (Reading database ... 15344 files and directories currently installed.) Removing libssl3:s390x (3.0.10-1ubuntu2) ... Selecting previously unselected package libssl3t64:s390x. (Reading database ... 15333 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.0.13-0ubuntu3_s390x.deb ... Unpacking libssl3t64:s390x (3.0.13-0ubuntu3) ... Setting up libssl3t64:s390x (3.0.13-0ubuntu3) ... (Reading database ... 15346 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_s390x.deb ... Unpacking systemd-sysv (255.4-1ubuntu5) over (253.5-1ubuntu6) ... Preparing to unpack .../systemd_255.4-1ubuntu5_s390x.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_s390x.deb ... Unpacking libsystemd0:s390x (255.4-1ubuntu5) over (253.5-1ubuntu6) ... Setting up libsystemd0:s390x (255.4-1ubuntu5) ... (Reading database ... 15485 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-5ubuntu4_s390x.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 ... 15484 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-5ubuntu4_s390x.deb ... Unpacking libpam-modules:s390x (1.5.3-5ubuntu4) over (1.5.2-6ubuntu1) ... dpkg: warning: unable to delete old directory '/lib/s390x-linux-gnu/security': Directory not empty Setting up libpam-modules:s390x (1.5.3-5ubuntu4) ... Installing new version of config file /etc/security/namespace.init ... dpkg: libhogweed6:s390x: dependency problems, but removing anyway as you requested: libgnutls30:s390x depends on libhogweed6 (>= 3.6). (Reading database ... 15481 files and directories currently installed.) Removing libhogweed6:s390x (3.9.1-2) ... dpkg: libnettle8:s390x: dependency problems, but removing anyway as you requested: libgnutls30:s390x depends on libnettle8 (>= 3.7~). Removing libnettle8:s390x (3.9.1-2) ... Selecting previously unselected package libnettle8t64:s390x. (Reading database ... 15469 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.9.1-2.2build1_s390x.deb ... Unpacking libnettle8t64:s390x (3.9.1-2.2build1) ... Setting up libnettle8t64:s390x (3.9.1-2.2build1) ... Selecting previously unselected package libhogweed6t64:s390x. (Reading database ... 15477 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2build1_s390x.deb ... Unpacking libhogweed6t64:s390x (3.9.1-2.2build1) ... Setting up libhogweed6t64:s390x (3.9.1-2.2build1) ... (Reading database ... 15483 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.3-4ubuntu1_s390x.deb ... Unpacking libp11-kit0:s390x (0.25.3-4ubuntu1) over (0.25.0-4ubuntu1) ... Setting up libp11-kit0:s390x (0.25.3-4ubuntu1) ... Selecting previously unselected package libunistring5:s390x. (Reading database ... 15483 files and directories currently installed.) Preparing to unpack .../libunistring5_1.1-2_s390x.deb ... Unpacking libunistring5:s390x (1.1-2) ... Setting up libunistring5:s390x (1.1-2) ... dpkg: libgnutls30:s390x: dependency problems, but removing anyway as you requested: apt depends on libgnutls30 (>= 3.7.5). (Reading database ... 15488 files and directories currently installed.) Removing libgnutls30:s390x (3.8.1-4ubuntu1) ... Selecting previously unselected package libgnutls30t64:s390x. (Reading database ... 15478 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu3_s390x.deb ... Unpacking libgnutls30t64:s390x (3.8.3-1.1ubuntu3) ... Setting up libgnutls30t64:s390x (3.8.3-1.1ubuntu3) ... dpkg: libapt-pkg6.0:s390x: dependency problems, but removing anyway as you requested: apt-utils depends on libapt-pkg6.0 (>= 2.7.3). apt depends on libapt-pkg6.0 (>= 2.7.3). (Reading database ... 15490 files and directories currently installed.) Removing libapt-pkg6.0:s390x (2.7.3) ... Selecting previously unselected package libapt-pkg6.0t64:s390x. (Reading database ... 15441 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.7.14_s390x.deb ... Unpacking libapt-pkg6.0t64:s390x (2.7.14) ... Setting up libapt-pkg6.0t64:s390x (2.7.14) ... (Reading database ... 15491 files and directories currently installed.) Preparing to unpack .../bzip2_1.0.8-5.1_s390x.deb ... Unpacking bzip2 (1.0.8-5.1) over (1.0.8-5build1) ... dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') Preparing to unpack .../libbz2-1.0_1.0.8-5.1_s390x.deb ... Unpacking libbz2-1.0:s390x (1.0.8-5.1) over (1.0.8-5build1) ... Setting up libbz2-1.0:s390x (1.0.8-5.1) ... Selecting previously unselected package gcc-14-base:s390x. (Reading database ... 15491 files and directories currently installed.) Preparing to unpack .../gcc-14-base_14-20240330-1ubuntu2_s390x.deb ... Unpacking gcc-14-base:s390x (14-20240330-1ubuntu2) ... Setting up gcc-14-base:s390x (14-20240330-1ubuntu2) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14-20240330-1ubuntu2_s390x.deb ... Unpacking libgcc-s1:s390x (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Setting up libgcc-s1:s390x (14-20240330-1ubuntu2) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libstdc++6_14-20240330-1ubuntu2_s390x.deb ... Unpacking libstdc++6:s390x (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Setting up libstdc++6:s390x (14-20240330-1ubuntu2) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libudev1_255.4-1ubuntu5_s390x.deb ... Unpacking libudev1:s390x (255.4-1ubuntu5) over (253.5-1ubuntu6) ... Setting up libudev1:s390x (255.4-1ubuntu5) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.2-2_s390x.deb ... Unpacking libxxhash0:s390x (0.8.2-2) over (0.8.1-1) ... Setting up libxxhash0:s390x (0.8.2-2) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1ubuntu2_s390x.deb ... Unpacking zlib1g:s390x (1:1.3.dfsg-3.1ubuntu2) over (1:1.2.13.dfsg-1ubuntu5) ... Setting up zlib1g:s390x (1:1.3.dfsg-3.1ubuntu2) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.6-1_s390x.deb ... Unpacking libffi8:s390x (3.4.6-1) over (3.4.4-1) ... Setting up libffi8:s390x (3.4.6-1) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.7-2_s390x.deb ... Unpacking libidn2-0:s390x (2.3.7-2) over (2.3.4-1) ... Setting up libidn2-0:s390x (2.3.7-2) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.271ubuntu3_s390x.deb ... Unpacking libdebconfclient0:s390x (0.271ubuntu3) over (0.270ubuntu1) ... Setting up libdebconfclient0:s390x (0.271ubuntu3) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../base-passwd_3.6.3_s390x.deb ... Unpacking base-passwd (3.6.3) over (3.6.1) ... Setting up base-passwd (3.6.3) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../libsqlite3-0_3.45.1-1ubuntu2_s390x.deb ... Unpacking libsqlite3-0:s390x (3.45.1-1ubuntu2) over (3.42.0-1) ... Preparing to unpack .../gpg_2.4.4-2ubuntu16_s390x.deb ... Unpacking gpg (2.4.4-2ubuntu16) over (2.2.40-1.1ubuntu1) ... dpkg: libreadline8:s390x: dependency problems, but removing anyway as you requested: gpgconf depends on libreadline8 (>= 6.0). (Reading database ... 15496 files and directories currently installed.) Removing libreadline8:s390x (8.2-1.3) ... Selecting previously unselected package libreadline8t64:s390x. (Reading database ... 15484 files and directories currently installed.) Preparing to unpack .../libreadline8t64_8.2-4build1_s390x.deb ... Adding 'diversion of /lib/s390x-linux-gnu/libhistory.so.8 to /lib/s390x-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/s390x-linux-gnu/libhistory.so.8.2 to /lib/s390x-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/s390x-linux-gnu/libreadline.so.8 to /lib/s390x-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/s390x-linux-gnu/libreadline.so.8.2 to /lib/s390x-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:s390x (8.2-4build1) ... Preparing to unpack .../readline-common_8.2-4build1_all.deb ... Unpacking readline-common (8.2-4build1) over (8.2-1.3) ... Preparing to unpack .../libncursesw6_6.4+20240113-1ubuntu1_s390x.deb ... Unpacking libncursesw6:s390x (6.4+20240113-1ubuntu1) over (6.4+20230625-2) ... Preparing to unpack .../libtinfo6_6.4+20240113-1ubuntu1_s390x.deb ... Unpacking libtinfo6:s390x (6.4+20240113-1ubuntu1) over (6.4+20230625-2) ... Setting up libtinfo6:s390x (6.4+20240113-1ubuntu1) ... (Reading database ... 15504 files and directories currently installed.) Preparing to unpack .../gpg-agent_2.4.4-2ubuntu16_s390x.deb ... Unpacking gpg-agent (2.4.4-2ubuntu16) over (2.2.40-1.1ubuntu1) ... Preparing to unpack .../gpgconf_2.4.4-2ubuntu16_s390x.deb ... Unpacking gpgconf (2.4.4-2ubuntu16) over (2.2.40-1.1ubuntu1) ... Preparing to unpack .../pinentry-curses_1.2.1-3ubuntu4_s390x.deb ... Unpacking pinentry-curses (1.2.1-3ubuntu4) over (1.2.1-1ubuntu1) ... Preparing to unpack .../init-system-helpers_1.66ubuntu1_all.deb ... Unpacking init-system-helpers (1.66ubuntu1) over (1.65.2ubuntu1) ... Setting up init-system-helpers (1.66ubuntu1) ... (Reading database ... 15503 files and directories currently installed.) Removing libnpth0:s390x (1.6-3build2) ... Selecting previously unselected package libnpth0t64:s390x. (Reading database ... 15498 files and directories currently installed.) Preparing to unpack .../libnpth0t64_1.6-3.1build1_s390x.deb ... Unpacking libnpth0t64:s390x (1.6-3.1build1) ... Setting up libnpth0t64:s390x (1.6-3.1build1) ... (Reading database ... 15504 files and directories currently installed.) Preparing to unpack .../gpgv_2.4.4-2ubuntu16_s390x.deb ... Unpacking gpgv (2.4.4-2ubuntu16) over (2.2.40-1.1ubuntu1) ... Setting up gpgv (2.4.4-2ubuntu16) ... (Reading database ... 15504 files and directories currently installed.) Preparing to unpack .../ubuntu-keyring_2023.11.28.1_all.deb ... Unpacking ubuntu-keyring (2023.11.28.1) over (2021.03.26) ... Setting up ubuntu-keyring (2023.11.28.1) ... (Reading database ... 15504 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-1ubuntu3_s390x.deb ... Unpacking libseccomp2:s390x (2.5.5-1ubuntu3) over (2.5.4-1ubuntu3) ... Setting up libseccomp2:s390x (2.5.5-1ubuntu3) ... (Reading database ... 15504 files and directories currently installed.) Preparing to unpack .../apt-utils_2.7.14_s390x.deb ... Unpacking apt-utils (2.7.14) over (2.7.3) ... Preparing to unpack .../archives/apt_2.7.14_s390x.deb ... Unpacking apt (2.7.14) over (2.7.3) ... Setting up apt (2.7.14) ... (Reading database ... 15504 files and directories currently installed.) Preparing to unpack .../debconf-i18n_1.5.86_all.deb ... Unpacking debconf-i18n (1.5.86) over (1.5.82) ... Preparing to unpack .../debconf_1.5.86_all.deb ... Unpacking debconf (1.5.86) over (1.5.82) ... Setting up debconf (1.5.86) ... Installing new version of config file /etc/debconf.conf ... (Reading database ... 15503 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.3-5ubuntu4_s390x.deb ... Unpacking libpam0g:s390x (1.5.3-5ubuntu4) over (1.5.2-6ubuntu1) ... Setting up libpam0g:s390x (1.5.3-5ubuntu4) ... (Reading database ... 15502 files and directories currently installed.) Preparing to unpack .../libargon2-1_0~20190702+dfsg-4_s390x.deb ... Unpacking libargon2-1:s390x (0~20190702+dfsg-4) over (0~20190702+dfsg-3) ... Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-3ubuntu3_s390x.deb ... Unpacking libdevmapper1.02.1:s390x (2:1.02.185-3ubuntu3) over (2:1.02.185-2ubuntu1) ... Preparing to unpack .../libuuid1_2.39.3-9ubuntu3_s390x.deb ... Unpacking libuuid1:s390x (2.39.3-9ubuntu3) over (2.39.1-4ubuntu2) ... Setting up libuuid1:s390x (2.39.3-9ubuntu3) ... (Reading database ... 15502 files and directories currently installed.) Preparing to unpack .../0-libfdisk1_2.39.3-9ubuntu3_s390x.deb ... Unpacking libfdisk1:s390x (2.39.3-9ubuntu3) over (2.39.1-4ubuntu2) ... Preparing to unpack .../1-mount_2.39.3-9ubuntu3_s390x.deb ... Unpacking mount (2.39.3-9ubuntu3) over (2.39.1-4ubuntu2) ... Preparing to unpack .../2-libcom-err2_1.47.0-2.4~exp1ubuntu3_s390x.deb ... Unpacking libcom-err2:s390x (1.47.0-2.4~exp1ubuntu3) over (1.47.0-2ubuntu1) ... Preparing to unpack .../3-libkeyutils1_1.6.3-3_s390x.deb ... Unpacking libkeyutils1:s390x (1.6.3-3) over (1.6.3-2) ... Preparing to unpack .../4-libnsl2_1.3.0-3build3_s390x.deb ... Unpacking libnsl2:s390x (1.3.0-3build3) over (1.3.0-2build2) ... Preparing to unpack .../5-linux-libc-dev_6.8.0-20.20_s390x.deb ... Unpacking linux-libc-dev:s390x (6.8.0-20.20) over (6.5.0-9.9) ... Preparing to unpack .../6-base-files_13ubuntu9_s390x.deb ... Unpacking base-files (13ubuntu9) over (13ubuntu3) ... Setting up base-files (13ubuntu9) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/update-motd.d/10-help-text ... (Reading database ... 15521 files and directories currently installed.) Preparing to unpack .../debianutils_5.17build1_s390x.deb ... Unpacking debianutils (5.17build1) over (5.8-1) ... Setting up debianutils (5.17build1) ... (Reading database ... 15520 files and directories currently installed.) Preparing to unpack .../bash_5.2.21-2ubuntu4_s390x.deb ... Unpacking bash (5.2.21-2ubuntu4) over (5.2.15-2ubuntu1) ... Setting up bash (5.2.21-2ubuntu4) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 15520 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.39.3-9ubuntu3_s390x.deb ... Unpacking bsdutils (1:2.39.3-9ubuntu3) over (1:2.39.1-4ubuntu2) ... Setting up bsdutils (1:2.39.3-9ubuntu3) ... (Reading database ... 15520 files and directories currently installed.) Removing usrmerge (35ubuntu1) ... (Reading database ... 15494 files and directories currently installed.) Preparing to unpack .../coreutils_9.4-3ubuntu5_s390x.deb ... Unpacking coreutils (9.4-3ubuntu5) over (9.1-1ubuntu2) ... Setting up coreutils (9.4-3ubuntu5) ... (Reading database ... 15499 files and directories currently installed.) Preparing to unpack .../tar_1.35+dfsg-3_s390x.deb ... Unpacking tar (1.35+dfsg-3) over (1.34+dfsg-1.2ubuntu1) ... Setting up tar (1.35+dfsg-3) ... (Reading database ... 15499 files and directories currently installed.) Preparing to unpack .../dpkg_1.22.6ubuntu6_s390x.deb ... Unpacking dpkg (1.22.6ubuntu6) over (1.22.0ubuntu1) ... Setting up dpkg (1.22.6ubuntu6) ... (Reading database ... 15497 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-6ubuntu5_s390x.deb ... Unpacking dash (0.5.12-6ubuntu5) over (0.5.12-6ubuntu1) ... Setting up dash (0.5.12-6ubuntu5) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.10-1_s390x.deb ... Unpacking diffutils (1:3.10-1) over (1:3.8-4) ... Setting up diffutils (1:3.10-1) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../archives/grep_3.11-4_s390x.deb ... Unpacking grep (3.11-4) over (3.11-2) ... Setting up grep (3.11-4) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../gzip_1.12-1ubuntu2_s390x.deb ... Unpacking gzip (1.12-1ubuntu2) over (1.12-1ubuntu1) ... dpkg: warning: old file '/bin/uncompress' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') dpkg: warning: old file '/bin/gunzip' is the same as several new files! (both '/usr/bin/gunzip' and '/usr/bin/uncompress') Setting up gzip (1.12-1ubuntu2) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../hostname_3.23+nmu2ubuntu1_s390x.deb ... Unpacking hostname (3.23+nmu2ubuntu1) over (3.23+nmu1ubuntu1) ... Setting up hostname (3.23+nmu2ubuntu1) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../login_1%3a4.13+dfsg1-4ubuntu1_s390x.deb ... Unpacking login (1:4.13+dfsg1-4ubuntu1) over (1:4.13+dfsg1-1ubuntu1) ... Setting up login (1:4.13+dfsg1-4ubuntu1) ... Installing new version of config file /etc/login.defs ... Installing new version of config file /etc/pam.d/login ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20240113-1ubuntu1_s390x.deb ... Unpacking ncurses-bin (6.4+20240113-1ubuntu1) over (6.4+20230625-2) ... Setting up ncurses-bin (6.4+20240113-1ubuntu1) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../archives/sed_4.9-2_s390x.deb ... Unpacking sed (4.9-2) over (4.9-1) ... Setting up sed (4.9-2) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../util-linux_2.39.3-9ubuntu3_s390x.deb ... Unpacking util-linux (2.39.3-9ubuntu3) over (2.39.1-4ubuntu2) ... Setting up util-linux (2.39.3-9ubuntu3) ... (Reading database ... 15498 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4+20240113-1ubuntu1_all.deb ... Unpacking ncurses-base (6.4+20240113-1ubuntu1) over (6.4+20230625-2) ... Setting up ncurses-base (6.4+20240113-1ubuntu1) ... (Reading database ... 15498 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.08-6ubuntu2_s390x.deb ... Unpacking sysvinit-utils (3.08-6ubuntu2) over (3.07-1ubuntu1) ... dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty dpkg: warning: unable to delete old directory '/lib/init': Directory not empty Setting up sysvinit-utils (3.08-6ubuntu2) ... (Reading database ... 15496 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-2.4~exp1ubuntu3_s390x.deb ... Unpacking logsave (1.47.0-2.4~exp1ubuntu3) over (1.47.0-2ubuntu1) ... dpkg: libext2fs2:s390x: dependency problems, but removing anyway as you requested: e2fsprogs depends on libext2fs2 (= 1.47.0-2ubuntu1). (Reading database ... 15496 files and directories currently installed.) Removing libext2fs2:s390x (1.47.0-2ubuntu1) ... Selecting previously unselected package libext2fs2t64:s390x. (Reading database ... 15489 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu3_s390x.deb ... Adding 'diversion of /lib/s390x-linux-gnu/libe2p.so.2 to /lib/s390x-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/s390x-linux-gnu/libe2p.so.2.3 to /lib/s390x-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/s390x-linux-gnu/libext2fs.so.2 to /lib/s390x-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/s390x-linux-gnu/libext2fs.so.2.4 to /lib/s390x-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:s390x (1.47.0-2.4~exp1ubuntu3) ... Setting up libcom-err2:s390x (1.47.0-2.4~exp1ubuntu3) ... Setting up libext2fs2t64:s390x (1.47.0-2.4~exp1ubuntu3) ... (Reading database ... 15505 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2.4~exp1ubuntu3_s390x.deb ... Unpacking e2fsprogs (1.47.0-2.4~exp1ubuntu3) over (1.47.0-2ubuntu1) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty Preparing to unpack .../optipng_0.7.8+ds-1build2_s390x.deb ... Unpacking optipng (0.7.8+ds-1build2) over (0.7.7-2build1) ... (Reading database ... 15503 files and directories currently installed.) Removing libpng16-16:s390x (1.6.40-1) ... Selecting previously unselected package libpng16-16t64:s390x. (Reading database ... 15493 files and directories currently installed.) Preparing to unpack .../libpng16-16t64_1.6.43-5build1_s390x.deb ... Unpacking libpng16-16t64:s390x (1.6.43-5build1) ... Setting up libapparmor1:s390x (4.0.0-beta3-0ubuntu3) ... Setting up libargon2-1:s390x (0~20190702+dfsg-4) ... Setting up libdevmapper1.02.1:s390x (2:1.02.185-3ubuntu3) ... Setting up libcryptsetup12:s390x (2:2.7.0-1ubuntu3) ... Setting up libfdisk1:s390x (2.39.3-9ubuntu3) ... Setting up libkmod2:s390x (31+20240202-2ubuntu5) ... Setting up libsystemd-shared:s390x (255.4-1ubuntu5) ... Setting up systemd-dev (255.4-1ubuntu6) ... Setting up mount (2.39.3-9ubuntu3) ... Setting up systemd (255.4-1ubuntu5) ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/pstore.conf ... Installing new version of config file /etc/systemd/sleep.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up systemd-sysv (255.4-1ubuntu5) ... (Reading database ... 15504 files and directories currently installed.) Preparing to unpack .../init_1.66ubuntu1_s390x.deb ... Unpacking init (1.66ubuntu1) over (1.65.2ubuntu1) ... Preparing to unpack .../libsmartcols1_2.39.3-9ubuntu3_s390x.deb ... Unpacking libsmartcols1:s390x (2.39.3-9ubuntu3) over (2.39.1-4ubuntu2) ... Setting up libsmartcols1:s390x (2.39.3-9ubuntu3) ... (Reading database ... 15505 files and directories currently installed.) Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu3_s390x.deb ... Unpacking uuid-runtime (2.39.3-9ubuntu3) over (2.39.1-4ubuntu2) ... dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty Preparing to unpack .../libattr1_1%3a2.5.2-1_s390x.deb ... Unpacking libattr1:s390x (1:2.5.2-1) over (1:2.5.1-4) ... Setting up libattr1:s390x (1:2.5.2-1) ... (Reading database ... 15503 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1_all.deb ... Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.1-1) ... Setting up libaudit-common (1:3.1.2-2.1) ... (Reading database ... 15503 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.4-2build2_s390x.deb ... Unpacking libcap-ng0:s390x (0.8.4-2build2) over (0.8.3-1build2) ... Setting up libcap-ng0:s390x (0.8.4-2build2) ... (Reading database ... 15503 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-2_s390x.deb ... Unpacking libmd0:s390x (1.1.0-2) over (1.1.0-1) ... Setting up libmd0:s390x (1.1.0-2) ... (Reading database ... 15503 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.5.3-5ubuntu4_all.deb ... Unpacking libpam-runtime (1.5.3-5ubuntu4) over (1.5.2-6ubuntu1) ... Setting up libpam-runtime (1.5.3-5ubuntu4) ... (Reading database ... 15502 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1build4_all.deb ... Unpacking libsemanage-common (3.5-1build4) over (3.5-1) ... Setting up libsemanage-common (3.5-1build4) ... (Reading database ... 15502 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-2_s390x.deb ... Unpacking libsepol2:s390x (3.5-2) over (3.5-1) ... Setting up libsepol2:s390x (3.5-2) ... (Reading database ... 15502 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1build4_s390x.deb ... Unpacking libsemanage2:s390x (3.5-1build4) over (3.5-1) ... Setting up libsemanage2:s390x (3.5-1build4) ... (Reading database ... 15502 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-4ubuntu1_s390x.deb ... Unpacking passwd (1:4.13+dfsg1-4ubuntu1) over (1:4.13+dfsg1-1ubuntu1) ... Setting up passwd (1:4.13+dfsg1-4ubuntu1) ... (Reading database ... 15502 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-4ubuntu3_s390x.deb ... Unpacking libproc2-0:s390x (2:4.0.4-4ubuntu3) over (2:4.0.3-1ubuntu1) ... Preparing to unpack .../01-libss2_1.47.0-2.4~exp1ubuntu3_s390x.deb ... Unpacking libss2:s390x (1.47.0-2.4~exp1ubuntu3) over (1.47.0-2ubuntu1) ... Preparing to unpack .../02-mawk_1.3.4.20240123-1_s390x.deb ... Unpacking mawk (1.3.4.20240123-1) over (1.3.4.20230730-1) ... Preparing to unpack .../03-procps_2%3a4.0.4-4ubuntu3_s390x.deb ... Unpacking procps (2:4.0.4-4ubuntu3) over (2:4.0.3-1ubuntu1) ... Preparing to unpack .../04-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) over (0.0.20) ... Preparing to unpack .../05-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) over (20230311ubuntu1) ... Preparing to unpack .../06-krb5-locales_1.20.1-6ubuntu1_all.deb ... Unpacking krb5-locales (1.20.1-6ubuntu1) over (1.20.1-3ubuntu1) ... Preparing to unpack .../07-tzdata_2024a-1ubuntu1_all.deb ... Unpacking tzdata (2024a-1ubuntu1) over (2023c-9ubuntu1) ... Preparing to unpack .../08-bash-completion_1%3a2.11-8_all.deb ... Unpacking bash-completion (1:2.11-8) over (1:2.11-7) ... Preparing to unpack .../09-bsdextrautils_2.39.3-9ubuntu3_s390x.deb ... Unpacking bsdextrautils (2.39.3-9ubuntu3) over (2.39.1-4ubuntu2) ... Preparing to unpack .../10-libgpm2_1.20.7-11_s390x.deb ... Unpacking libgpm2:s390x (1.20.7-11) over (1.20.7-10build1) ... Preparing to unpack .../11-libip4tc2_1.8.10-3ubuntu1_s390x.deb ... Unpacking libip4tc2:s390x (1.8.10-3ubuntu1) over (1.8.9-2ubuntu2) ... Preparing to unpack .../12-libjansson4_2.14-2build2_s390x.deb ... Unpacking libjansson4:s390x (2.14-2build2) over (2.14-2) ... Preparing to unpack .../13-psmisc_23.7-1build1_s390x.deb ... Unpacking psmisc (23.7-1build1) over (23.6-1) ... Preparing to unpack .../14-xz-utils_5.6.1+really5.4.5-1build1_s390x.deb ... Unpacking xz-utils (5.6.1+really5.4.5-1build1) over (5.4.1-0.2) ... Preparing to unpack .../15-libctf0_2.42-4ubuntu2_s390x.deb ... Unpacking libctf0:s390x (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../16-libctf-nobfd0_2.42-4ubuntu2_s390x.deb ... Unpacking libctf-nobfd0:s390x (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../17-binutils-s390x-linux-gnu_2.42-4ubuntu2_s390x.deb ... Unpacking binutils-s390x-linux-gnu (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../18-libbinutils_2.42-4ubuntu2_s390x.deb ... Unpacking libbinutils:s390x (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../19-binutils_2.42-4ubuntu2_s390x.deb ... Unpacking binutils (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../20-binutils-common_2.42-4ubuntu2_s390x.deb ... Unpacking binutils-common:s390x (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../21-libsframe1_2.42-4ubuntu2_s390x.deb ... Unpacking libsframe1:s390x (2.42-4ubuntu2) over (2.41-5ubuntu1) ... Preparing to unpack .../22-libubsan1_14-20240330-1ubuntu2_s390x.deb ... Unpacking libubsan1:s390x (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Preparing to unpack .../23-libgomp1_14-20240330-1ubuntu2_s390x.deb ... Unpacking libgomp1:s390x (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Preparing to unpack .../24-libitm1_14-20240330-1ubuntu2_s390x.deb ... Unpacking libitm1:s390x (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Preparing to unpack .../25-libatomic1_14-20240330-1ubuntu2_s390x.deb ... Unpacking libatomic1:s390x (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Preparing to unpack .../26-libasan8_14-20240330-1ubuntu2_s390x.deb ... Unpacking libasan8:s390x (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Preparing to unpack .../27-g++-13_13.2.0-23ubuntu3_s390x.deb ... Unpacking g++-13 (13.2.0-23ubuntu3) over (13.2.0-4ubuntu3) ... Preparing to unpack .../28-gcc-13_13.2.0-23ubuntu3_s390x.deb ... Unpacking gcc-13 (13.2.0-23ubuntu3) over (13.2.0-4ubuntu3) ... Preparing to unpack .../29-libstdc++-13-dev_13.2.0-23ubuntu3_s390x.deb ... Unpacking libstdc++-13-dev:s390x (13.2.0-23ubuntu3) over (13.2.0-4ubuntu3) ... Preparing to unpack .../30-libgcc-13-dev_13.2.0-23ubuntu3_s390x.deb ... Unpacking libgcc-13-dev:s390x (13.2.0-23ubuntu3) over (13.2.0-4ubuntu3) ... Preparing to unpack .../31-libcc1-0_14-20240330-1ubuntu2_s390x.deb ... Unpacking libcc1-0:s390x (14-20240330-1ubuntu2) over (13.2.0-4ubuntu3) ... Preparing to unpack .../32-cpp-13_13.2.0-23ubuntu3_s390x.deb ... Unpacking cpp-13 (13.2.0-23ubuntu3) over (13.2.0-4ubuntu3) ... Preparing to unpack .../33-gcc-13-base_13.2.0-23ubuntu3_s390x.deb ... Unpacking gcc-13-base:s390x (13.2.0-23ubuntu3) over (13.2.0-4ubuntu3) ... Selecting previously unselected package gcc-13-s390x-linux-gnu. Preparing to unpack .../34-gcc-13-s390x-linux-gnu_13.2.0-23ubuntu3_s390x.deb ... Unpacking gcc-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Selecting previously unselected package g++-13-s390x-linux-gnu. Preparing to unpack .../35-g++-13-s390x-linux-gnu_13.2.0-23ubuntu3_s390x.deb ... Unpacking g++-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Selecting previously unselected package cpp-13-s390x-linux-gnu. Preparing to unpack .../36-cpp-13-s390x-linux-gnu_13.2.0-23ubuntu3_s390x.deb ... Unpacking cpp-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Preparing to unpack .../37-g++_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking g++ (4:13.2.0-7ubuntu1) over (4:13.2.0-1ubuntu1) ... Preparing to unpack .../38-gcc_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking gcc (4:13.2.0-7ubuntu1) over (4:13.2.0-1ubuntu1) ... Preparing to unpack .../39-cpp_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking cpp (4:13.2.0-7ubuntu1) over (4:13.2.0-1ubuntu1) ... Selecting previously unselected package cpp-s390x-linux-gnu. Preparing to unpack .../40-cpp-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Selecting previously unselected package gcc-s390x-linux-gnu. Preparing to unpack .../41-gcc-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Selecting previously unselected package g++-s390x-linux-gnu. Preparing to unpack .../42-g++-s390x-linux-gnu_4%3a13.2.0-7ubuntu1_s390x.deb ... Unpacking g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Preparing to unpack .../43-dpkg-dev_1.22.6ubuntu6_all.deb ... Unpacking dpkg-dev (1.22.6ubuntu6) over (1.22.0ubuntu1) ... Preparing to unpack .../44-libdpkg-perl_1.22.6ubuntu6_all.deb ... Unpacking libdpkg-perl (1.22.6ubuntu6) over (1.22.0ubuntu1) ... Preparing to unpack .../45-lto-disabled-list_47_all.deb ... Unpacking lto-disabled-list (47) over (43) ... Preparing to unpack .../46-libfakeroot_1.33-1_s390x.deb ... Unpacking libfakeroot:s390x (1.33-1) over (1.32.1-1) ... Preparing to unpack .../47-fakeroot_1.33-1_s390x.deb ... Unpacking fakeroot (1.33-1) over (1.32.1-1) ... Setting up libip4tc2:s390x (1.8.10-3ubuntu1) ... Setting up libtext-iconv-perl:s390x (1.7-8build3) ... Setting up libtext-charwidth-perl:s390x (0.04-11build3) ... Setting up libkeyutils1:s390x (1.6.3-3) ... Setting up lto-disabled-list (47) ... Setting up libgpm2:s390x (1.20.7-11) ... Setting up libgdbm6t64:s390x (1.23-5.1build1) ... Setting up bsdextrautils (2.39.3-9ubuntu3) ... Setting up init (1.66ubuntu1) ... Setting up libgdbm-compat4t64:s390x (1.23-5.1build1) ... Setting up psmisc (23.7-1build1) ... Setting up libtirpc-common (1.3.4+ds-1.1build1) ... Setting up libsqlite3-0:s390x (3.45.1-1ubuntu2) ... Setting up binutils-common:s390x (2.42-4ubuntu2) ... Setting up linux-libc-dev:s390x (6.8.0-20.20) ... Setting up libctf-nobfd0:s390x (2.42-4ubuntu2) ... Setting up krb5-locales (1.20.1-6ubuntu1) ... Setting up libgomp1:s390x (14-20240330-1ubuntu2) ... Setting up bzip2 (1.0.8-5.1) ... Setting up libsframe1:s390x (2.42-4ubuntu2) ... Setting up libfakeroot:s390x (1.33-1) ... Setting up libjansson4:s390x (2.14-2build2) ... Setting up libkrb5support0:s390x (1.20.1-6ubuntu2) ... Setting up tzdata (2024a-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Mar 31 21:43:00 UTC 2024. Universal Time is now: Sun Mar 31 21:43:00 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... Setting up gcc-13-base:s390x (13.2.0-23ubuntu3) ... Setting up cpp-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Setting up bash-completion (1:2.11-8) ... Setting up xz-utils (5.6.1+really5.4.5-1build1) ... Setting up perl-modules-5.38 (5.38.2-3.2build1) ... Setting up libproc2-0:s390x (2:4.0.4-4ubuntu3) ... Setting up libpng16-16t64:s390x (1.6.43-5build1) ... Setting up libatomic1:s390x (14-20240330-1ubuntu2) ... Setting up libss2:s390x (1.47.0-2.4~exp1ubuntu3) ... Setting up libncursesw6:s390x (6.4+20240113-1ubuntu1) ... Setting up libk5crypto3:s390x (1.20.1-6ubuntu2) ... Setting up logsave (1.47.0-2.4~exp1ubuntu3) ... Setting up libdb5.3t64:s390x (5.3.28+dfsg2-6build1) ... Setting up libubsan1:s390x (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:s390x (1:4.4.36-4) ... Setting up libasan8:s390x (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:s390x (1.20.1-6ubuntu2) ... Setting up libperl5.38t64:s390x (5.38.2-3.2build1) ... Setting up libbinutils:s390x (2.42-4ubuntu2) ... Setting up libc-dev-bin (2.39-0ubuntu8) ... 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:s390x (14-20240330-1ubuntu2) ... Setting up liblocale-gettext-perl (1.07-6ubuntu5) ... Setting up libitm1:s390x (14-20240330-1ubuntu2) ... Setting up libctf0:s390x (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu4) ... Setting up apt-utils (2.7.14) ... Setting up binutils-s390x-linux-gnu (2.42-4ubuntu2) ... Setting up cpp-13 (13.2.0-23ubuntu3) ... Setting up cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up debconf-i18n (1.5.86) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu3) ... Setting up binutils (2.42-4ubuntu2) ... 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:s390x (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu6) ... Setting up libreadline8t64:s390x (8.2-4build1) ... Setting up libgcc-13-dev:s390x (13.2.0-23ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu16) ... Setting up libc6-dev:s390x (2.39-0ubuntu8) ... Setting up gpg (2.4.4-2ubuntu16) ... Setting up libstdc++-13-dev:s390x (13.2.0-23ubuntu3) ... Setting up gpg-agent (2.4.4-2ubuntu16) ... Setting up libtirpc3t64:s390x (1.3.4+ds-1.1build1) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up libtirpc-dev:s390x (1.3.4+ds-1.1build1) ... Setting up gcc-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13-s390x-linux-gnu (13.2.0-23ubuntu3) ... Setting up gcc-13 (13.2.0-23ubuntu3) ... Setting up libnsl2:s390x (1.3.0-3build3) ... Setting up g++-13 (13.2.0-23ubuntu3) ... Setting up g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:s390x (1.3-5) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:s390x (1.3.0-3build3) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15548 files and directories currently installed.) Purging configuration files for libssl3:s390x (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-27988875 s390x noble-proposed -c chroot:build-PACKAGEBUILD-27988875 --arch=s390x --dist=noble-proposed --nolog htslib_1.19+ds-1.1build3.dsc Initiating build PACKAGEBUILD-27988875 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:49 UTC 2024 s390x sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-s390x-006.buildd +==============================================================================+ | htslib 1.19+ds-1.1build3 (s390x) Sun, 31 Mar 2024 21:43:03 +0000 | +==============================================================================+ Package: htslib Version: 1.19+ds-1.1build3 Source Version: 1.19+ds-1.1build3 Distribution: noble-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27988875/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/htslib-9yZ9Ti/resolver-Q5k2Pd' 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-9yZ9Ti/htslib-1.19+ds' with '<>' I: NOTICE: Log filtering will replace 'build/htslib-9yZ9Ti' 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 [516 B] Fetched 1907 B in 0s (0 B/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 27.5 MB of archives. After this operation, 94.7 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 s390x libelf1t64 s390x 0.190-1.1build3 [69.6 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libicu74 s390x 74.2-1ubuntu1 [10.9 MB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxml2 s390x 2.9.14+dfsg-1.3ubuntu3 [818 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmagic-mgc s390x 1:5.45-3build1 [305 kB] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libmagic1t64 s390x 1:5.45-3build1 [93.2 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x file s390x 1:5.45-3build1 [22.2 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main s390x gettext-base s390x 0.21-14ubuntu1 [39.4 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libuchardet0 s390x 0.0.8-1 [76.1 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main s390x groff-base s390x 1.23.0-3build2 [1049 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libnghttp2-14 s390x 1.59.0-1build2 [77.8 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpipeline1 s390x 1.5.7-2 [25.0 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libpsl5t64 s390x 0.21.2-1.1build1 [57.7 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main s390x man-db s390x 2.12.0-4build1 [1253 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main s390x m4 s390x 1.4.19-4 [255 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x autoconf all 2.71-3 [339 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x autotools-dev all 20220109.1 [44.9 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x autopoint all 0.21-14ubuntu1 [422 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x libtool all 2.4.7-7 [166 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main s390x dh-autoreconf all 20 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libsub-override-perl all 0.10-1 [10.0 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main s390x dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libdw1t64 s390x 0.190-1.1build3 [286 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main s390x debugedit s390x 1:5.0-5build1 [50.5 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main s390x dwz s390x 0.15-1build5 [122 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x gettext s390x 0.21-14ubuntu1 [917 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main s390x debhelper all 13.14.1ubuntu5 [869 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main s390x libbrotli1 s390x 1.1.0-2build1 [375 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libbz2-dev s390x 1.0.8-5.1 [39.4 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsasl2-modules-db s390x 2.1.28+dfsg1-5ubuntu2 [21.2 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsasl2-2 s390x 2.1.28+dfsg1-5ubuntu2 [57.8 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libldap2 s390x 2.6.7+dfsg-1~exp1ubuntu7 [202 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build7 [58.4 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main s390x libssh-4 s390x 0.10.6-2build1 [189 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcurl3t64-gnutls s390x 8.5.0-2ubuntu9 [356 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libcurl4-gnutls-dev s390x 8.5.0-2ubuntu9 [466 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate-dev s390x 1.19-1 [52.4 kB] Get:45 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] Get:46 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs-dev s390x 1.6.0-1 [2981 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl-dev s390x 3.0.13-0ubuntu3 [2131 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main s390x zlib1g-dev s390x 1:1.3.dfsg-3.1ubuntu2 [904 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main s390x liblzma-dev s390x 5.6.1+really5.4.5-1build1 [184 kB] Preconfiguring packages ... Fetched 27.5 MB in 2s (13.3 MB/s) Selecting previously unselected package libelf1t64:s390x. (Reading database ... 15548 files and directories currently installed.) Preparing to unpack .../00-libelf1t64_0.190-1.1build3_s390x.deb ... Unpacking libelf1t64:s390x (0.190-1.1build3) ... Selecting previously unselected package libicu74:s390x. Preparing to unpack .../01-libicu74_74.2-1ubuntu1_s390x.deb ... Unpacking libicu74:s390x (74.2-1ubuntu1) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.3ubuntu3_s390x.deb ... Unpacking libxml2:s390x (2.9.14+dfsg-1.3ubuntu3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3build1_s390x.deb ... Unpacking libmagic-mgc (1:5.45-3build1) ... Selecting previously unselected package libmagic1t64:s390x. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3build1_s390x.deb ... Unpacking libmagic1t64:s390x (1:5.45-3build1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3build1_s390x.deb ... Unpacking file (1:5.45-3build1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14ubuntu1_s390x.deb ... Unpacking gettext-base (0.21-14ubuntu1) ... Selecting previously unselected package libuchardet0:s390x. Preparing to unpack .../07-libuchardet0_0.0.8-1_s390x.deb ... Unpacking libuchardet0:s390x (0.0.8-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-3build2_s390x.deb ... Unpacking groff-base (1.23.0-3build2) ... Selecting previously unselected package libnghttp2-14:s390x. Preparing to unpack .../09-libnghttp2-14_1.59.0-1build2_s390x.deb ... Unpacking libnghttp2-14:s390x (1.59.0-1build2) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../10-libpipeline1_1.5.7-2_s390x.deb ... Unpacking libpipeline1:s390x (1.5.7-2) ... Selecting previously unselected package libpsl5t64:s390x. Preparing to unpack .../11-libpsl5t64_0.21.2-1.1build1_s390x.deb ... Unpacking libpsl5t64:s390x (0.21.2-1.1build1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.12.0-4build1_s390x.deb ... Unpacking man-db (2.12.0-4build1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_s390x.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.5-1.3ubuntu1_all.deb ... Unpacking automake (1:1.16.5-1.3ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-14ubuntu1_all.deb ... Unpacking autopoint (0.21-14ubuntu1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.14.1ubuntu5_all.deb ... Unpacking libdebhelper-perl (13.14.1ubuntu5) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../22-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../23-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../24-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libdw1t64:s390x. Preparing to unpack .../25-libdw1t64_0.190-1.1build3_s390x.deb ... Unpacking libdw1t64:s390x (0.190-1.1build3) ... Selecting previously unselected package debugedit. Preparing to unpack .../26-debugedit_1%3a5.0-5build1_s390x.deb ... Unpacking debugedit (1:5.0-5build1) ... Selecting previously unselected package dwz. Preparing to unpack .../27-dwz_0.15-1build5_s390x.deb ... Unpacking dwz (0.15-1build5) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-14ubuntu1_s390x.deb ... Unpacking gettext (0.21-14ubuntu1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.14.1ubuntu5_all.deb ... Unpacking debhelper (13.14.1ubuntu5) ... Selecting previously unselected package libbrotli1:s390x. Preparing to unpack .../32-libbrotli1_1.1.0-2build1_s390x.deb ... Unpacking libbrotli1:s390x (1.1.0-2build1) ... Selecting previously unselected package libbz2-dev:s390x. Preparing to unpack .../33-libbz2-dev_1.0.8-5.1_s390x.deb ... Unpacking libbz2-dev:s390x (1.0.8-5.1) ... Selecting previously unselected package libsasl2-modules-db:s390x. Preparing to unpack .../34-libsasl2-modules-db_2.1.28+dfsg1-5ubuntu2_s390x.deb ... Unpacking libsasl2-modules-db:s390x (2.1.28+dfsg1-5ubuntu2) ... Selecting previously unselected package libsasl2-2:s390x. Preparing to unpack .../35-libsasl2-2_2.1.28+dfsg1-5ubuntu2_s390x.deb ... Unpacking libsasl2-2:s390x (2.1.28+dfsg1-5ubuntu2) ... Selecting previously unselected package libldap2:s390x. Preparing to unpack .../36-libldap2_2.6.7+dfsg-1~exp1ubuntu7_s390x.deb ... Unpacking libldap2:s390x (2.6.7+dfsg-1~exp1ubuntu7) ... Selecting previously unselected package librtmp1:s390x. Preparing to unpack .../37-librtmp1_2.4+20151223.gitfa8646d.1-2build7_s390x.deb ... Unpacking librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build7) ... Selecting previously unselected package libssh-4:s390x. Preparing to unpack .../38-libssh-4_0.10.6-2build1_s390x.deb ... Unpacking libssh-4:s390x (0.10.6-2build1) ... Selecting previously unselected package libcurl3t64-gnutls:s390x. Preparing to unpack .../39-libcurl3t64-gnutls_8.5.0-2ubuntu9_s390x.deb ... Unpacking libcurl3t64-gnutls:s390x (8.5.0-2ubuntu9) ... Selecting previously unselected package libcurl4-gnutls-dev:s390x. Preparing to unpack .../40-libcurl4-gnutls-dev_8.5.0-2ubuntu9_s390x.deb ... Unpacking libcurl4-gnutls-dev:s390x (8.5.0-2ubuntu9) ... Selecting previously unselected package libdeflate0:s390x. Preparing to unpack .../41-libdeflate0_1.19-1_s390x.deb ... Unpacking libdeflate0:s390x (1.19-1) ... Selecting previously unselected package libdeflate-dev:s390x. Preparing to unpack .../42-libdeflate-dev_1.19-1_s390x.deb ... Unpacking libdeflate-dev:s390x (1.19-1) ... Selecting previously unselected package libhtscodecs2:s390x. Preparing to unpack .../43-libhtscodecs2_1.6.0-1_s390x.deb ... Unpacking libhtscodecs2:s390x (1.6.0-1) ... Selecting previously unselected package libhtscodecs-dev:s390x. Preparing to unpack .../44-libhtscodecs-dev_1.6.0-1_s390x.deb ... Unpacking libhtscodecs-dev:s390x (1.6.0-1) ... Selecting previously unselected package libssl-dev:s390x. Preparing to unpack .../45-libssl-dev_3.0.13-0ubuntu3_s390x.deb ... Unpacking libssl-dev:s390x (3.0.13-0ubuntu3) ... Selecting previously unselected package zlib1g-dev:s390x. Preparing to unpack .../46-zlib1g-dev_1%3a1.3.dfsg-3.1ubuntu2_s390x.deb ... Unpacking zlib1g-dev:s390x (1:1.3.dfsg-3.1ubuntu2) ... Selecting previously unselected package liblzma-dev:s390x. Preparing to unpack .../47-liblzma-dev_5.6.1+really5.4.5-1build1_s390x.deb ... Unpacking liblzma-dev:s390x (5.6.1+really5.4.5-1build1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../48-sbuild-build-depends-main-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:s390x (1.6.0-1) ... Setting up libpipeline1:s390x (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:s390x (1.1.0-2build1) ... Setting up libmagic1t64:s390x (1:5.45-3build1) ... Setting up libpsl5t64:s390x (0.21.2-1.1build1) ... Setting up libnghttp2-14:s390x (1.59.0-1build2) ... Setting up libdeflate0:s390x (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:s390x (0.190-1.1build3) ... Setting up libdw1t64:s390x (0.190-1.1build3) ... Setting up libsasl2-modules-db:s390x (2.1.28+dfsg1-5ubuntu2) ... Setting up libhtscodecs-dev:s390x (1.6.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build7) ... Setting up libssl-dev:s390x (3.0.13-0ubuntu3) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up libsasl2-2:s390x (2.1.28+dfsg1-5ubuntu2) ... Setting up libssh-4:s390x (0.10.6-2build1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:s390x (5.6.1+really5.4.5-1build1) ... Setting up libicu74:s390x (74.2-1ubuntu1) ... Setting up zlib1g-dev:s390x (1:1.3.dfsg-3.1ubuntu2) ... Setting up dwz (0.15-1build5) ... Setting up libuchardet0:s390x (0.0.8-1) ... Setting up debugedit (1:5.0-5build1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libdeflate-dev:s390x (1.19-1) ... Setting up libxml2:s390x (2.9.14+dfsg-1.3ubuntu3) ... Setting up libldap2:s390x (2.6.7+dfsg-1~exp1ubuntu7) ... Setting up libbz2-dev:s390x (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:s390x (8.5.0-2ubuntu9) ... Setting up libcurl4-gnutls-dev:s390x (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 (s390x included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:49 UTC 2024 s390x (s390x) 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-s390x-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-s390x-linux-gnu_13.2.0-23ubuntu3 cpp-s390x-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-s390x-linux-gnu_13.2.0-23ubuntu3 g++-s390x-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-s390x-linux-gnu_13.2.0-23ubuntu3 gcc-14-base_14-20240330-1ubuntu2 gcc-s390x-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 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 libreadline8t64_8.2-4build1 librtmp1_2.4+20151223.gitfa8646d.1-2build7 libsasl2-2_2.1.28+dfsg1-5ubuntu2 libsasl2-modules-db_2.1.28+dfsg1-5ubuntu2 libseccomp2_2.5.5-1ubuntu3 libselinux1_3.5-2ubuntu2 libsemanage-common_3.5-1build4 libsemanage2_3.5-1build4 libsepol2_3.5-2 libsframe1_2.42-4ubuntu2 libsmartcols1_2.39.3-9ubuntu3 libsqlite3-0_3.45.1-1ubuntu2 libss2_1.47.0-2.4~exp1ubuntu3 libssh-4_0.10.6-2build1 libssl-dev_3.0.13-0ubuntu3 libssl3t64_3.0.13-0ubuntu3 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 libsub-override-perl_0.10-1 libsystemd-shared_255.4-1ubuntu5 libsystemd0_255.4-1ubuntu5 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11build3 libtext-iconv-perl_1.7-8build3 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20240113-1ubuntu1 libtirpc-common_1.3.4+ds-1.1build1 libtirpc-dev_1.3.4+ds-1.1build1 libtirpc3t64_1.3.4+ds-1.1build1 libtool_2.4.7-7 libubsan1_14-20240330-1ubuntu2 libuchardet0_0.0.8-1 libudev1_255.4-1ubuntu5 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-9ubuntu3 libxml2_2.9.14+dfsg-1.3ubuntu3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.0-20.20 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-4ubuntu1 logsave_1.47.0-2.4~exp1ubuntu3 lto-disabled-list_47 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-4build1 mawk_1.3.4.20240123-1 mount_2.39.3-9ubuntu3 ncurses-base_6.4+20240113-1ubuntu1 ncurses-bin_6.4+20240113-1ubuntu1 openssl_3.0.13-0ubuntu3 optipng_0.7.8+ds-1build2 passwd_1:4.13+dfsg1-4ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3.2build1 perl-base_5.38.2-3.2build1 perl-modules-5.36_5.36.0-9ubuntu1 perl-modules-5.38_5.38.2-3.2build1 pinentry-curses_1.2.1-3ubuntu4 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-4ubuntu3 psmisc_23.7-1build1 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 systemd_255.4-1ubuntu5 systemd-dev_255.4-1ubuntu6 systemd-sysv_255.4-1ubuntu5 sysvinit-utils_3.08-6ubuntu2 tar_1.35+dfsg-3 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-9ubuntu3 uuid-runtime_2.39.3-9ubuntu3 xz-utils_5.6.1+really5.4.5-1build1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: htslib Binary: libhts3t64, libhts-dev, htslib-test, tabix Architecture: any all Version: 1.19+ds-1.1build3 Maintainer: Ubuntu Developers Uploaders: Charles Plessy , Andreas Tille , Michael R. Crusoe , Steffen Moeller , Étienne Mollier Homepage: https://github.com/samtools/htslib Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/htslib Vcs-Git: https://salsa.debian.org/med-team/htslib.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@, build-essential Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), libbz2-dev, libcurl4-gnutls-dev, liblzma-dev, libssl-dev, zlib1g-dev, libdeflate-dev, libhtscodecs-dev (>= 1.0) Package-List: htslib-test deb science optional arch=all libhts-dev deb libdevel optional arch=any libhts3t64 deb libs optional arch=any tabix deb science optional arch=any Checksums-Sha1: 33b65ea5de06a41c42cf8ef0d74f7ef7e4739408 1522390 htslib_1.19+ds.orig.tar.bz2 82a8183deb3e8fc927d8afe7255d4063f2ff4db6 21420 htslib_1.19+ds-1.1build3.debian.tar.xz Checksums-Sha256: e740e5a68db806a4c8252009348da5f0cc1bcdd134f702e4e1cce724e855f777 1522390 htslib_1.19+ds.orig.tar.bz2 37ebea6ed0e05d77181265ace97b1ee646127a6ef613a33faa1d3b8f50295d27 21420 htslib_1.19+ds-1.1build3.debian.tar.xz Files: 79efd7a83fdd5a36a3d8057180681ec0 1522390 htslib_1.19+ds.orig.tar.bz2 46b8056d01f089f97e8fd8c6494d52fd 21420 htslib_1.19+ds-1.1build3.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQJOBAEBCgA4FiEErEg/aN5yj0PyIC/KVo0w8yGyEz0FAmYJqrcaHHN0ZXZlLmxh bmdhc2VrQHVidW50dS5jb20ACgkQVo0w8yGyEz1D1Q//Qg6GHX0MdVYYhcXvD+TN 3XjqBXXhPqBHSfLrIuJvpDdyomsxxmNZa46ZIBuhgsJbecAug+AdnKQn/5V88B98 1V+4TQZDhYKV1Oh5ijUukOdiTNMWDFA91OqbW2dCLmE3qVa/K87IrYItwlUw8Nwp PsKx8Ck5aSfbqXJkxM1P9Ji282N13rJ7EMge7kO7h2JuFatCp59oNqRE1RIjw9pi Q+wFO/tAJ1NPJ7B1JZcHL/pI7mERI6gwV1tiP1dPW+cB+4A5Y7luiP0EkZ1cxcsV wIHLHuqajHzAYsr3TGPPy91xMOsMNkfm1QBJ+SekIK6F93/7Y+ygHwXaZbNjj9mo ejtC0UdQp3fVzLEmH2p8VRnpGDv5jwDMmu6bjA1VGvrxoIuKrH9L59hGaqdkCCtp rlSkFSbhhEtmSKeyybOFEsn1pu5H7zSQ8LbtqQSQMyPlxnHgexUKjfAmiXwXJ5Lv 0UDu12M9fjfc0sLVgnXV+oZPl6daKb7/Tp2rvYSkXH4azRJoWRkYIPcpmwKPcJI8 bA9TLhZtviHa8652ixs4FeHP6Vmo8D1CUxUI18SOapTWX13WLn/ucTBOtjNpchyh fPKXKtJOf/ckFxEi3aUmvRIF69OXWndBhnkxiZ24/TzdpxAbPl+b5/bWjdUQynXX w48Q3I/kjQOTA9gpbf+7vxU= =ULfj -----END PGP SIGNATURE----- gpgv: Signature made Sun Mar 31 18:25:59 2024 UTC gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./htslib_1.19+ds-1.1build3.dsc: no acceptable signature found dpkg-source: info: extracting htslib in /<> dpkg-source: info: unpacking htslib_1.19+ds.orig.tar.bz2 dpkg-source: info: unpacking htslib_1.19+ds-1.1build3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_git_version dpkg-source: info: applying define_PATH_MAX.patch dpkg-source: info: applying fPIC.patch dpkg-source: info: applying testShebang.patch dpkg-source: info: applying fix_float_precision dpkg-source: info: applying cram_to_bam_export.patch dpkg-source: info: applying fix_sequence_of_linked_libs.patch dpkg-source: info: applying trim-file-prefix.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27988875 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27988875 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27988875 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 s390x 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/s390x-linux-gnu/htslib' \ --with-external-htscodecs \ --with-plugin-path='/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/s390x-linux-gnu/htslib' ./configure --build=s390x-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/s390x-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-libcurl --enable-gcs --enable-s3 --enable-plugins --with-plugin-dir=/usr/lib/s390x-linux-gnu/htslib --with-external-htscodecs --with-plugin-path=/usr/local/lib/htslib:/usr/local/libexec/htslib:/usr/lib/s390x-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... s390x-ibm-linux-gnu checking host system type... s390x-ibm-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/s390x-linux-gnu make -j4 "CFLAGS=-g -O2 -fno-omit-frame-pointer -mbackchain -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/s390x-linux-gnu make[2]: Entering directory '/<>' gcc -g -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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/s390x-linux-gnu/htslib\" -c -o plugin.o plugin.c gcc -g -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 bcf_sr_sort.pico bcf_sr_sort.c gcc -g -O2 -fno-omit-frame-pointer -mbackchain -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 bgzf.pico bgzf.c gcc -g -O2 -fno-omit-frame-pointer -mbackchain -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 errmod.pico errmod.c gcc -g -O2 -fno-omit-frame-pointer -mbackchain -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 faidx.pico faidx.c gcc -g -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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/s390x-linux-gnu/htslib\" -fPIC -c -o plugin.pico plugin.c gcc -g -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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 -O2 -fno-omit-frame-pointer -mbackchain -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/s390x-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 -O2 -fno-omit-frame-pointer -mbackchain -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/s390x-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/4BOzhHiHpC/index.bam.csi /<>/test/index.sam > /tmp/4BOzhHiHpC/index.bam .. ok test_index: /<>/test/test_index -c /tmp/4BOzhHiHpC/index.bam .. ok test_index: /<>/test/test_view -l 0 -b -m 0 -x /tmp/4BOzhHiHpC/index.bam.bai /<>/test/index.sam > /tmp/4BOzhHiHpC/index.bam .. ok test_index: /<>/test/test_index -b /tmp/4BOzhHiHpC/index.bam .. ok test_index: /<>/test/test_view -l 0 -z -m 14 -x /tmp/4BOzhHiHpC/index.sam.gz.csi /<>/test/index.sam > /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 0 -x /tmp/4BOzhHiHpC/index.sam.gz.bai /<>/test/index.sam > /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 14 -x /tmp/4BOzhHiHpC/index.sam.gz.csi /<>/test/index_dos.sam > /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 0 -x /tmp/4BOzhHiHpC/index.sam.gz.bai /<>/test/index_dos.sam > /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_view -l 0 -C -x /tmp/4BOzhHiHpC/index.cram.crai /<>/test/index.sam > /tmp/4BOzhHiHpC/index.cram .. ok test_index: /<>/test/test_index /tmp/4BOzhHiHpC/index.cram .. ok test_index: /<>/test/test_view -l 0 -b -m 14 -x /tmp/4BOzhHiHpC/index.bcf.csi /<>/test/index.vcf > /tmp/4BOzhHiHpC/index.bcf .. ok test_index: /<>/test/test_index -c /tmp/4BOzhHiHpC/index.bcf .. ok test_index: /<>/test/test_view -l 0 -z -m 14 -x /tmp/4BOzhHiHpC/index.vcf.gz.csi /<>/test/index.vcf > /tmp/4BOzhHiHpC/index.vcf.gz .. ok test_index: /<>/test/test_index -c /tmp/4BOzhHiHpC/index.vcf.gz .. ok test_index: /<>/test/test_view -l 0 -z -m 0 -x /tmp/4BOzhHiHpC/index.vcf.gz.tbi /<>/test/index.vcf > /tmp/4BOzhHiHpC/index.vcf.gz .. ok test_index: /<>/test/test_index -t /tmp/4BOzhHiHpC/index.vcf.gz .. ok test_index: /<>/tabix /tmp/4BOzhHiHpC/index.vcf.gz##idx##/tmp/4BOzhHiHpC/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /<>/test/test_view /tmp/4BOzhHiHpC/index2.bam 1:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/4BOzhHiHpC/index2.bam 1:2000000-2000000 .. ok test_index: /<>/test/test_view /tmp/4BOzhHiHpC/index2.bam 2:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/4BOzhHiHpC/index2.bam 2:2000000-2000000 .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/4BOzhHiHpC/index.bam.csi /<>/test/index.sam > /tmp/4BOzhHiHpC/index.bam .. ok test_index: /<>/test/test_index -c /tmp/4BOzhHiHpC/index.bam .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 0 -x /tmp/4BOzhHiHpC/index.bam.bai /<>/test/index.sam > /tmp/4BOzhHiHpC/index.bam .. ok test_index: /<>/test/test_index -b /tmp/4BOzhHiHpC/index.bam .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/4BOzhHiHpC/index.sam.gz.csi /<>/test/index.sam > /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/4BOzhHiHpC/index.sam.gz.bai /<>/test/index.sam > /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/4BOzhHiHpC/index.sam.gz.csi /<>/test/index_dos.sam > /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_index -c /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/4BOzhHiHpC/index.sam.gz.bai /<>/test/index_dos.sam > /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_index -b /tmp/4BOzhHiHpC/index.sam.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -C -x /tmp/4BOzhHiHpC/index.cram.crai /<>/test/index.sam > /tmp/4BOzhHiHpC/index.cram .. ok test_index: /<>/test/test_index /tmp/4BOzhHiHpC/index.cram .. ok test_index: /<>/test/test_view -@4 -l 0 -b -m 14 -x /tmp/4BOzhHiHpC/index.bcf.csi /<>/test/index.vcf > /tmp/4BOzhHiHpC/index.bcf .. ok test_index: /<>/test/test_index -c /tmp/4BOzhHiHpC/index.bcf .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 14 -x /tmp/4BOzhHiHpC/index.vcf.gz.csi /<>/test/index.vcf > /tmp/4BOzhHiHpC/index.vcf.gz .. ok test_index: /<>/test/test_index -c /tmp/4BOzhHiHpC/index.vcf.gz .. ok test_index: /<>/test/test_view -@4 -l 0 -z -m 0 -x /tmp/4BOzhHiHpC/index.vcf.gz.tbi /<>/test/index.vcf > /tmp/4BOzhHiHpC/index.vcf.gz .. ok test_index: /<>/test/test_index -t /tmp/4BOzhHiHpC/index.vcf.gz .. ok test_index: /<>/tabix /tmp/4BOzhHiHpC/index.vcf.gz##idx##/tmp/4BOzhHiHpC/index.vcf.gz.tbi 1:10000060-10000060 .. ok test_index: /<>/test/test_view /tmp/4BOzhHiHpC/index2.bam 1:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/4BOzhHiHpC/index2.bam 1:2000000-2000000 .. ok test_index: /<>/test/test_view /tmp/4BOzhHiHpC/index2.bam 2:1000000-1000000 .. ok test_index: /<>/test/test_view /tmp/4BOzhHiHpC/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/4BOzhHiHpC/test-vcf-api.bcf .. ok test_bcf2vcf: /<>/test/test_view /<>/test/tabix/vcf_file.bcf .. ok test_vcf_sweep: /<>/test/test-vcf-sweep /tmp/4BOzhHiHpC/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/4BOzhHiHpC -s 74452500 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/4BOzhHiHpC -s 34270147 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/4BOzhHiHpC -s 11108528 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/4BOzhHiHpC -s 42233895 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/4BOzhHiHpC -s 8111117 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/4BOzhHiHpC -s 85644070 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/4BOzhHiHpC -s 49879942 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/4BOzhHiHpC -s 47881429 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/4BOzhHiHpC -s 69081244 .. ok test-bcf-sr: /<>/test/test-bcf-sr.pl -t /tmp/4BOzhHiHpC -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/4BOzhHiHpC/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/4BOzhHiHpC/no_index_2.out 2> /tmp/4BOzhHiHpC/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/4BOzhHiHpC/no_index_3.out 2> /tmp/4BOzhHiHpC/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/4BOzhHiHpC/no_index_4.out 2> /tmp/4BOzhHiHpC/no_index_4.err (expected fail) .. ok test_bcf_sr_range: /<>/test/test_view -b -p /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf -x /tmp/4BOzhHiHpC/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/4BOzhHiHpC/range_test_1.out.vcf -r '1' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_2.out.vcf -r '1:1-2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_3.out.vcf -r '1:1,1:2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_4.out.vcf -r '1:1-1' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_5.out.vcf -r '{1:1}' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_6.out.vcf -r '{1:1}:1-2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_7.out.vcf -r '{1:1}:1,{1:1}:2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_8.out.vcf -r '{1:1}:1-1' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_9.out.vcf -r '{1:1-1}' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_10.out.vcf -r '{1:1-1}:1-2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_11.out.vcf -r '{1:1-1}:1,{1:1-1}:2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_12.out.vcf -r '{1:1-1}:1-1' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_13.out.vcf -r '{1:1-1}-2' --args /tmp/4BOzhHiHpC/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/4BOzhHiHpC/range_test_14.out.vcf -t '1' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_15.out.vcf -t '1:1-2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_16.out.vcf -t '1:1,1:2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_17.out.vcf -t '1:1-1' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_18.out.vcf -t '{1:1}' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_19.out.vcf -t '{1:1}:1-2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_20.out.vcf -t '{1:1}:1,{1:1}:2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_21.out.vcf -t '{1:1}:1-1' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_22.out.vcf -t '{1:1-1}' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_23.out.vcf -t '{1:1-1}:1-2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_24.out.vcf -t '{1:1-1}:1,{1:1-1}:2' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_25.out.vcf -t '{1:1-1}:1-1' --args /tmp/4BOzhHiHpC/weird-chr-names.vcf.bcf .. ok test_bcf_sr_range: /<>/test/test-bcf-sr -O vcf -o /tmp/4BOzhHiHpC/range_test_26.out.vcf -t '{1:1-1}-2' --args /tmp/4BOzhHiHpC/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/4BOzhHiHpC/headernul0.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/4BOzhHiHpC/headernul1.bam .. ok test_convert_padded_header: /<>/test/test_view -t ce.fa -C /tmp/4BOzhHiHpC/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-2JXo4pxi 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/s390x-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 -O2 -fno-omit-frame-pointer -mbackchain -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/s390x-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/s390x-linux-gnu /<>/debian/tmp/usr/share/man/man1 /<>/debian/tmp/usr/share/man/man5 /<>/debian/tmp/usr/share/man/man7 /<>/debian/tmp/usr/lib/s390x-linux-gnu/pkgconfig if test -n "/usr/lib/s390x-linux-gnu/htslib"; then mkdir -p -m 755 /<>/debian/tmp/usr/lib/s390x-linux-gnu/htslib; fi install -p -m 644 libhts.so /<>/debian/tmp/usr/lib/s390x-linux-gnu/libhts.so.1.19 sed -e 's#@-includedir@#/usr/include#g;s#@-libdir@#/usr/lib/s390x-linux-gnu#g;s#@-PACKAGE_VERSION@#1.19#g' htslib.pc.tmp > /<>/debian/tmp/usr/lib/s390x-linux-gnu/pkgconfig/htslib.pc chmod 644 /<>/debian/tmp/usr/lib/s390x-linux-gnu/pkgconfig/htslib.pc ln -sf libhts.so.1.19 /<>/debian/tmp/usr/lib/s390x-linux-gnu/libhts.so ln -sf libhts.so.1.19 /<>/debian/tmp/usr/lib/s390x-linux-gnu/libhts.so.3 install -p annot-tsv bgzip htsfile tabix /<>/debian/tmp/usr/bin if test -n "hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so"; then install -p hfile_libcurl.so hfile_gcs.so hfile_s3.so hfile_s3_write.so /<>/debian/tmp/usr/lib/s390x-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/s390x-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/s390x-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/s390x-linux-gnu/htslib debian/tmp/usr/lib/s390x-linux-gnu/libhts.so.1.19 debian/tmp/usr/lib/s390x-linux-gnu/libhts.so.3 debian/libhts3t64/usr/lib/s390x-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/s390x-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/s390x-linux-gnu/libhts.a debian/tmp/usr/lib/s390x-linux-gnu/libhts.so debian/libhts-dev/usr/lib/s390x-linux-gnu/ install -m0755 -d debian/libhts-dev/usr/lib/s390x-linux-gnu/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/s390x-linux-gnu/pkgconfig/htslib.pc debian/libhts-dev/usr/lib/s390x-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/s390x-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/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 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 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/faidx.5.dh-new debian/libhts3t64/usr/share/man/man5/faidx.5 mv debian/libhts3t64/usr/share/man/man5/sam.5.dh-new debian/libhts3t64/usr/share/man/man5/sam.5 chmod 0644 -- debian/libhts3t64/usr/share/man/man5/faidx.5 debian/libhts3t64/usr/share/man/man5/sam.5 mv debian/libhts3t64/usr/share/man/man5/vcf.5.dh-new debian/libhts3t64/usr/share/man/man5/vcf.5 mv debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7.dh-new debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 chmod 0644 -- debian/libhts3t64/usr/share/man/man5/vcf.5 debian/libhts3t64/usr/share/man/man7/htslib-s3-plugin.7 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/s390x-linux-gnu/libhts.so.3 ln -s libhts.so.1.19 debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.3 rm -f debian/libhts-dev/usr/lib/s390x-linux-gnu/libhts.so ln -s libhts.so.1.19 debian/libhts-dev/usr/lib/s390x-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/libhts3t64/changelog usr/share/doc/libhts3t64/changelog.Debian usr/share/man/man5/faidx.5 usr/share/man/man5/sam.5 usr/share/man/man5/vcf.5 usr/share/man/man7/htslib-s3-plugin.7 chmod a-x usr/share/doc/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/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/libhts-dev/README.large_positions.md usr/share/doc/libhts-dev/changelog usr/share/doc/libhts-dev/changelog.Debian 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 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/tabix ! -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/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/tabix/usr/share/doc -type f -a -true -a ! -regex 'debian/tabix/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libhts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/tabix/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libhts3t64/usr/share/man debian/libhts3t64/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts3t64 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libhts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/tabix -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/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/s390x-linux-gnu dwz -mdebian/libhts3t64/usr/lib/debug/.dwz/s390x-linux-gnu/libhts3t64.debug -M/usr/lib/debug/.dwz/s390x-linux-gnu/libhts3t64.debug -- debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19 install -m0755 -d debian/tabix/usr/lib/debug/.dwz/s390x-linux-gnu dwz -mdebian/tabix/usr/lib/debug/.dwz/s390x-linux-gnu/tabix.debug -M/usr/lib/debug/.dwz/s390x-linux-gnu/tabix.debug -- debian/tabix/usr/bin/bgzip debian/tabix/usr/bin/htsfile debian/tabix/usr/bin/tabix dwz: debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19: DWARF compression not beneficial - old size 959125 new size 969861 objcopy --compress-debug-sections debian/libhts3t64/usr/lib/debug/.dwz/s390x-linux-gnu/libhts3t64.debug chmod 0644 -- debian/libhts3t64/usr/lib/debug/.dwz/s390x-linux-gnu/libhts3t64.debug objcopy --compress-debug-sections debian/tabix/usr/lib/debug/.dwz/s390x-linux-gnu/tabix.debug chmod 0644 -- debian/tabix/usr/lib/debug/.dwz/s390x-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/s390x-linux-gnu/libhts.so.1.19 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_0x1f21 d5c76b5838a15352610c33f8f2657d201a75a6d1 7bcc0a62d9f75b78d89ed10aff411e8cf7ce09ce install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d5 objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/bgzip debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d5/c76b5838a15352610c33f8f2657d201a75a6d1.debug install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7b objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19 debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7b/cc0a62d9f75b78d89ed10aff411e8cf7ce09ce.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d5/c76b5838a15352610c33f8f2657d201a75a6d1.debug strip --remove-section=.comment --remove-section=.note -o /tmp/Vev6oZmblM/stripspf3_6 debian/tabix/usr/bin/bgzip chmod --reference debian/tabix/usr/bin/bgzip /tmp/Vev6oZmblM/stripspf3_6 cat '/tmp/Vev6oZmblM/stripspf3_6' > 'debian/tabix/usr/bin/bgzip' chmod --reference /tmp/Vev6oZmblM/stripspf3_6 debian/tabix/usr/bin/bgzip objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/d5/c76b5838a15352610c33f8f2657d201a75a6d1.debug debian/tabix/usr/bin/bgzip /tmp/Vev6oZmblM/objcopytVVc9U chmod --reference debian/tabix/usr/bin/bgzip /tmp/Vev6oZmblM/objcopytVVc9U cat '/tmp/Vev6oZmblM/objcopytVVc9U' > 'debian/tabix/usr/bin/bgzip' chmod --reference /tmp/Vev6oZmblM/objcopytVVc9U debian/tabix/usr/bin/bgzip 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 cf1b81c26f7c50dcab0725155ad3ec4b8f0efc20 install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cf objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/tabix debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cf/1b81c26f7c50dcab0725155ad3ec4b8f0efc20.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7b/cc0a62d9f75b78d89ed10aff411e8cf7ce09ce.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/n3eMIZ4X17/stripmTos1a debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19 chmod --reference debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19 /tmp/n3eMIZ4X17/stripmTos1a cat '/tmp/n3eMIZ4X17/stripmTos1a' > 'debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19' chmod --reference /tmp/n3eMIZ4X17/stripmTos1a debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19 objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/7b/cc0a62d9f75b78d89ed10aff411e8cf7ce09ce.debug debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19 /tmp/n3eMIZ4X17/objcopyMGCi8R chmod --reference debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19 /tmp/n3eMIZ4X17/objcopyMGCi8R cat '/tmp/n3eMIZ4X17/objcopyMGCi8R' > 'debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19' chmod --reference /tmp/n3eMIZ4X17/objcopyMGCi8R debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19 debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so debugedit: debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so: Unknown DWARF DW_FORM_0x1f21 0153f9ef56fcdd1b21da0b08d20e10d736df3ce9 install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/01 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/01/53f9ef56fcdd1b21da0b08d20e10d736df3ce9.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/01/53f9ef56fcdd1b21da0b08d20e10d736df3ce9.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/n3eMIZ4X17/stripd385kE debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so chmod --reference debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so /tmp/n3eMIZ4X17/stripd385kE cat '/tmp/n3eMIZ4X17/stripd385kE' > 'debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so' chmod --reference /tmp/n3eMIZ4X17/stripd385kE debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/01/53f9ef56fcdd1b21da0b08d20e10d736df3ce9.debug debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so /tmp/n3eMIZ4X17/objcopy3p7V1X chmod --reference debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so /tmp/n3eMIZ4X17/objcopy3p7V1X cat '/tmp/n3eMIZ4X17/objcopy3p7V1X' > 'debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so' chmod --reference /tmp/n3eMIZ4X17/objcopy3p7V1X debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so debugedit: debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so: Unknown DWARF DW_FORM_0x1f20 79244e8bf08f95a49b45d6056140846a4a070c28 install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/79 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/79/244e8bf08f95a49b45d6056140846a4a070c28.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/79/244e8bf08f95a49b45d6056140846a4a070c28.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/n3eMIZ4X17/strip_xkUX1 debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so chmod --reference debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so /tmp/n3eMIZ4X17/strip_xkUX1 cat '/tmp/n3eMIZ4X17/strip_xkUX1' > 'debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so' chmod --reference /tmp/n3eMIZ4X17/strip_xkUX1 debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/79/244e8bf08f95a49b45d6056140846a4a070c28.debug debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so /tmp/n3eMIZ4X17/objcopypYq3X6 chmod --reference debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so /tmp/n3eMIZ4X17/objcopypYq3X6 cat '/tmp/n3eMIZ4X17/objcopypYq3X6' > 'debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so' chmod --reference /tmp/n3eMIZ4X17/objcopypYq3X6 debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so debugedit: debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so: Unknown DWARF DW_FORM_0x1f20 1967daa7cb93260a41c69649c13ac6cb50edefdb install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/19 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/19/67daa7cb93260a41c69649c13ac6cb50edefdb.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/19/67daa7cb93260a41c69649c13ac6cb50edefdb.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/n3eMIZ4X17/striprA8Y9n debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so chmod --reference debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so /tmp/n3eMIZ4X17/striprA8Y9n cat '/tmp/n3eMIZ4X17/striprA8Y9n' > 'debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so' chmod --reference /tmp/n3eMIZ4X17/striprA8Y9n debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/19/67daa7cb93260a41c69649c13ac6cb50edefdb.debug debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so /tmp/n3eMIZ4X17/objcopyvR2pA5 chmod --reference debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so /tmp/n3eMIZ4X17/objcopyvR2pA5 cat '/tmp/n3eMIZ4X17/objcopyvR2pA5' > 'debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so' chmod --reference /tmp/n3eMIZ4X17/objcopyvR2pA5 debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so debugedit --build-id --build-id-seed=libhts3t64/1.19\+ds-1.1build3 debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so debugedit: debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so: Unknown DWARF DW_FORM_0x1f20 e118101a5c8dd4f8b6c29fc0eefc4b31efac9fa6 install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/e1 objcopy --only-keep-debug --compress-debug-sections debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/e1/18101a5c8dd4f8b6c29fc0eefc4b31efac9fa6.debug chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/e1/18101a5c8dd4f8b6c29fc0eefc4b31efac9fa6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded -o /tmp/n3eMIZ4X17/stripJKwzdX debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so chmod --reference debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so /tmp/n3eMIZ4X17/stripJKwzdX cat '/tmp/n3eMIZ4X17/stripJKwzdX' > 'debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so' chmod --reference /tmp/n3eMIZ4X17/stripJKwzdX debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so objcopy --add-gnu-debuglink debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.build-id/e1/18101a5c8dd4f8b6c29fc0eefc4b31efac9fa6.debug debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so /tmp/n3eMIZ4X17/objcopyAFCHFp chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cf/1b81c26f7c50dcab0725155ad3ec4b8f0efc20.debug strip --remove-section=.comment --remove-section=.note -o /tmp/Vev6oZmblM/stripSCYrJV debian/tabix/usr/bin/tabix chmod --reference debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so /tmp/n3eMIZ4X17/objcopyAFCHFp cat '/tmp/n3eMIZ4X17/objcopyAFCHFp' > 'debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so' chmod --reference debian/tabix/usr/bin/tabix /tmp/Vev6oZmblM/stripSCYrJV chmod --reference /tmp/n3eMIZ4X17/objcopyAFCHFp debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so cat '/tmp/Vev6oZmblM/stripSCYrJV' > 'debian/tabix/usr/bin/tabix' install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/libhts3t64/usr/lib/debug/.dwz/s390x-linux-gnu debian/.debhelper/libhts3t64/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/libhts3t64/usr/lib/debug/.dwz chmod --reference /tmp/Vev6oZmblM/stripSCYrJV debian/tabix/usr/bin/tabix rmdir -p --ignore-fail-on-non-empty debian/libhts3t64/usr/lib/debug objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/cf/1b81c26f7c50dcab0725155ad3ec4b8f0efc20.debug debian/tabix/usr/bin/tabix /tmp/Vev6oZmblM/objcopyFV2h8F 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 --reference debian/tabix/usr/bin/tabix /tmp/Vev6oZmblM/objcopyFV2h8F cat '/tmp/Vev6oZmblM/objcopyFV2h8F' > 'debian/tabix/usr/bin/tabix' chmod --reference /tmp/Vev6oZmblM/objcopyFV2h8F debian/tabix/usr/bin/tabix 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_0x1f20 6a08d44608c69e41f39bc8ceffe13579f22c59c8 install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/6a objcopy --only-keep-debug --compress-debug-sections debian/tabix/usr/bin/htsfile debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/6a/08d44608c69e41f39bc8ceffe13579f22c59c8.debug chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/6a/08d44608c69e41f39bc8ceffe13579f22c59c8.debug strip --remove-section=.comment --remove-section=.note -o /tmp/Vev6oZmblM/stripB_TGwJ debian/tabix/usr/bin/htsfile chmod --reference debian/tabix/usr/bin/htsfile /tmp/Vev6oZmblM/stripB_TGwJ cat '/tmp/Vev6oZmblM/stripB_TGwJ' > 'debian/tabix/usr/bin/htsfile' chmod --reference /tmp/Vev6oZmblM/stripB_TGwJ debian/tabix/usr/bin/htsfile objcopy --add-gnu-debuglink debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.build-id/6a/08d44608c69e41f39bc8ceffe13579f22c59c8.debug debian/tabix/usr/bin/htsfile /tmp/Vev6oZmblM/objcopyu4JO82 chmod --reference debian/tabix/usr/bin/htsfile /tmp/Vev6oZmblM/objcopyu4JO82 cat '/tmp/Vev6oZmblM/objcopyu4JO82' > 'debian/tabix/usr/bin/htsfile' chmod --reference /tmp/Vev6oZmblM/objcopyu4JO82 debian/tabix/usr/bin/htsfile install -m0755 -d debian/.debhelper/tabix/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/tabix/usr/lib/debug/.dwz/s390x-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/s390x-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/bgzip debian/tabix/usr/bin/tabix debian/tabix/usr/bin/htsfile install -m0755 -d debian/libhts3t64/DEBIAN dpkg-shlibdeps -Tdebian/libhts3t64.substvars debian/libhts3t64/usr/lib/s390x-linux-gnu/libhts.so.1.19 debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_s3.so debian/libhts3t64/usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.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/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/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=0153f9ef56fcdd1b21da0b08d20e10d736df3ce9 1967daa7cb93260a41c69649c13ac6cb50edefdb 79244e8bf08f95a49b45d6056140846a4a070c28 7bcc0a62d9f75b78d89ed10aff411e8cf7ce09ce e118101a5c8dd4f8b6c29fc0eefc4b31efac9fa6" -DSection=debug -DPackage-Type=ddeb -UReplaces -UBreaks 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=6a08d44608c69e41f39bc8ceffe13579f22c59c8 cf1b81c26f7c50dcab0725155ad3ec4b8f0efc20 d5c76b5838a15352610c33f8f2657d201a75a6d1" -DSection=debug -DPackage-Type=ddeb -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/libhts-dev/DEBIAN/control chmod 0644 -- debian/.debhelper/tabix/dbgsym-root/DEBIAN/control dpkg-gencontrol -ptabix -ldebian/changelog -Tdebian/tabix.substvars -Pdebian/tabix chmod 0644 -- debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibhts3t64 -ldebian/changelog -Tdebian/libhts3t64.substvars -Pdebian/libhts3t64 chmod 0644 -- debian/tabix/DEBIAN/control chmod 0644 -- debian/libhts3t64/DEBIAN/control dh_md5sums -a install -m0755 -d debian/libhts3t64/DEBIAN install -m0755 -d debian/tabix/DEBIAN install -m0755 -d debian/libhts-dev/DEBIAN cd debian/tabix >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhts3t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libhts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libhts3t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libhts3t64/dbgsym-root/DEBIAN chmod 0644 -- debian/tabix/DEBIAN/md5sums install -m0755 -d debian/.debhelper/tabix/dbgsym-root/DEBIAN cd debian/.debhelper/libhts3t64/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/tabix/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.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 pkgstripfiles: processing control file: debian/libhts-dev/DEBIAN/control, package libhts-dev, directory debian/libhts-dev .. removing usr/share/doc/libhts-dev/changelog.gz INFO: pkgstripfiles: waiting for lock (libhts-dev) ... pkgstripfiles: processing control file: debian/.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_s390x.deb'. Renaming tabix-dbgsym_1.19+ds-1.1build3_s390x.deb to tabix-dbgsym_1.19+ds-1.1build3_s390x.ddeb mv debian/.debhelper/scratch-space/build-tabix/tabix-dbgsym_1.19\+ds-1.1build3_s390x.deb ../tabix-dbgsym_1.19\+ds-1.1build3_s390x.ddeb INFO: pkgstripfiles: waiting for lock (libhts-dev) ... INFO: pkgstripfiles: waiting for lock (libhts-dev) ... INFO: pkgstripfiles: waiting for lock (libhts-dev) ... INFO: pkgstripfiles: waiting for lock (libhts-dev) ... pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com INFO: pkgstripfiles: waiting for lock (libhts-dev) ... pkgstripfiles: processing control file: debian/libhts3t64/DEBIAN/control, package libhts3t64, directory debian/libhts3t64 .. removing usr/share/doc/libhts3t64/changelog.gz pkgstripfiles: Running PNG optimization (using 4 cpus) for package libhts3t64 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libhts3t64' in '../libhts3t64_1.19+ds-1.1build3_s390x.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/libhts3t64/dbgsym-root debian/.debhelper/scratch-space/build-libhts3t64 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libhts3t64-dbgsym (in debian/.debhelper/libhts3t64/dbgsym-root); do_strip: , oemstrip: 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_s390x.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_s390x.deb'. Renaming libhts3t64-dbgsym_1.19+ds-1.1build3_s390x.deb to libhts3t64-dbgsym_1.19+ds-1.1build3_s390x.ddeb mv debian/.debhelper/scratch-space/build-libhts3t64/libhts3t64-dbgsym_1.19\+ds-1.1build3_s390x.deb ../libhts3t64-dbgsym_1.19\+ds-1.1build3_s390x.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_s390x.deb'. dpkg-genbuildinfo --build=any -O../htslib_1.19+ds-1.1build3_s390x.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../htslib_1.19+ds-1.1build3_s390x.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 2024-03-31T21:47:15Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ htslib_1.19+ds-1.1build3_s390x.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: s390x 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: aadc0dd1440b8655e4ccb37c851e82b1b91b39b5 7671 htslib_1.19+ds-1.1build3_s390x.buildinfo 212d08ca7e23cdca65941aacd9d4abe25fc4bc4c 5961954 libhts-dev_1.19+ds-1.1build3_s390x.deb e9d7acea596c8fd936b03c321fa468dca960716e 1288790 libhts3t64-dbgsym_1.19+ds-1.1build3_s390x.ddeb 8575cd29a035ab83786be06fc0f2adf5a2ee9e96 474226 libhts3t64_1.19+ds-1.1build3_s390x.deb b9ae1d2d88f1b24346db377952cae785e549ce94 2836780 tabix-dbgsym_1.19+ds-1.1build3_s390x.ddeb 6586ec2cf29b6cc9deb90356a5fa2aff60edd2ed 542634 tabix_1.19+ds-1.1build3_s390x.deb Checksums-Sha256: 301ee73fde15bd2a262a73ff88b3105aed8801c1875a92bb243a8f37b913b65a 7671 htslib_1.19+ds-1.1build3_s390x.buildinfo 7e27982a05707b7f18507c5adf058eb1b825583f4322018d852cedf2123566d0 5961954 libhts-dev_1.19+ds-1.1build3_s390x.deb 5b263ba745c408c5255741283c57e44a42992ba4d31d2874becacb48efdd4f5a 1288790 libhts3t64-dbgsym_1.19+ds-1.1build3_s390x.ddeb 8d34604167a8f4cda934208b99eafa0e4ea3433dd616d57fba98b7bc52495edf 474226 libhts3t64_1.19+ds-1.1build3_s390x.deb 1d44481b55e6e7ccc2166c49346a2a57006cbd2e462519dd16428ffdafc6a6b4 2836780 tabix-dbgsym_1.19+ds-1.1build3_s390x.ddeb 56cfad937b0378a4ebd8de5b6820eb6dba4bbe5cad7063dba0ef539011a20467 542634 tabix_1.19+ds-1.1build3_s390x.deb Files: f225751cf6e807586137cb53dca7347c 7671 science optional htslib_1.19+ds-1.1build3_s390x.buildinfo f11db05e9c485fb903fafe418c4dbc84 5961954 libdevel optional libhts-dev_1.19+ds-1.1build3_s390x.deb 381ff57fc821e88854219def0459ea98 1288790 debug optional libhts3t64-dbgsym_1.19+ds-1.1build3_s390x.ddeb 7cdb001cdc5464a4d05da185127cbb82 474226 libs optional libhts3t64_1.19+ds-1.1build3_s390x.deb 4e5d0b7a521a05c142db676d043a02a6 2836780 debug optional tabix-dbgsym_1.19+ds-1.1build3_s390x.ddeb 6dfccb54c65de54a0e384c42eb4a7e57 542634 science optional tabix_1.19+ds-1.1build3_s390x.deb Original-Maintainer: Debian Med Packaging Team /<>/htslib_1.19+ds-1.1build3_s390x.changes.new could not be renamed to /<>/htslib_1.19+ds-1.1build3_s390x.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: htslib Binary: libhts-dev libhts3t64 libhts3t64-dbgsym tabix tabix-dbgsym Architecture: s390x Version: 1.19+ds-1.1build3 Checksums-Md5: f11db05e9c485fb903fafe418c4dbc84 5961954 libhts-dev_1.19+ds-1.1build3_s390x.deb 381ff57fc821e88854219def0459ea98 1288790 libhts3t64-dbgsym_1.19+ds-1.1build3_s390x.ddeb 7cdb001cdc5464a4d05da185127cbb82 474226 libhts3t64_1.19+ds-1.1build3_s390x.deb 4e5d0b7a521a05c142db676d043a02a6 2836780 tabix-dbgsym_1.19+ds-1.1build3_s390x.ddeb 6dfccb54c65de54a0e384c42eb4a7e57 542634 tabix_1.19+ds-1.1build3_s390x.deb Checksums-Sha1: 212d08ca7e23cdca65941aacd9d4abe25fc4bc4c 5961954 libhts-dev_1.19+ds-1.1build3_s390x.deb e9d7acea596c8fd936b03c321fa468dca960716e 1288790 libhts3t64-dbgsym_1.19+ds-1.1build3_s390x.ddeb 8575cd29a035ab83786be06fc0f2adf5a2ee9e96 474226 libhts3t64_1.19+ds-1.1build3_s390x.deb b9ae1d2d88f1b24346db377952cae785e549ce94 2836780 tabix-dbgsym_1.19+ds-1.1build3_s390x.ddeb 6586ec2cf29b6cc9deb90356a5fa2aff60edd2ed 542634 tabix_1.19+ds-1.1build3_s390x.deb Checksums-Sha256: 7e27982a05707b7f18507c5adf058eb1b825583f4322018d852cedf2123566d0 5961954 libhts-dev_1.19+ds-1.1build3_s390x.deb 5b263ba745c408c5255741283c57e44a42992ba4d31d2874becacb48efdd4f5a 1288790 libhts3t64-dbgsym_1.19+ds-1.1build3_s390x.ddeb 8d34604167a8f4cda934208b99eafa0e4ea3433dd616d57fba98b7bc52495edf 474226 libhts3t64_1.19+ds-1.1build3_s390x.deb 1d44481b55e6e7ccc2166c49346a2a57006cbd2e462519dd16428ffdafc6a6b4 2836780 tabix-dbgsym_1.19+ds-1.1build3_s390x.ddeb 56cfad937b0378a4ebd8de5b6820eb6dba4bbe5cad7063dba0ef539011a20467 542634 tabix_1.19+ds-1.1build3_s390x.deb Build-Origin: Ubuntu Build-Architecture: s390x Build-Date: Sun, 31 Mar 2024 21:47:15 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu9), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), binutils-s390x-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-s390x-linux-gnu (= 13.2.0-23ubuntu3), cpp-s390x-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-s390x-linux-gnu (= 13.2.0-23ubuntu3), g++-s390x-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-s390x-linux-gnu (= 13.2.0-23ubuntu3), gcc-14-base (= 14-20240330-1ubuntu2), gcc-s390x-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), 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), 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), 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_s390x.deb -------------------------------------- new Debian package, version 2.0. size 5961954 bytes: control archive=1906 bytes. 1312 bytes, 28 lines control 2194 bytes, 34 lines md5sums Package: libhts-dev Source: htslib Version: 1.19+ds-1.1build3 Architecture: s390x Maintainer: Ubuntu Developers Installed-Size: 12224 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/s390x-linux-gnu/ -rw-r--r-- root/root 11991418 2024-03-31 18:25 ./usr/lib/s390x-linux-gnu/libhts.a lrwxrwxrwx root/root 0 2024-03-31 18:25 ./usr/lib/s390x-linux-gnu/libhts.so -> libhts.so.1.19 drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/lib/s390x-linux-gnu/pkgconfig/ -rw-r--r-- root/root 782 2024-03-31 18:25 ./usr/lib/s390x-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_s390x.deb -------------------------------------- new Debian package, version 2.0. size 474226 bytes: control archive=6137 bytes. 1399 bytes, 25 lines control 877 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: s390x Maintainer: Ubuntu Developers Installed-Size: 1171 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/s390x-linux-gnu/ drwxr-xr-x root/root 0 2024-03-31 18:25 ./usr/lib/s390x-linux-gnu/htslib/ -rw-r--r-- root/root 10248 2024-03-31 18:25 ./usr/lib/s390x-linux-gnu/htslib/hfile_gcs.so -rw-r--r-- root/root 34824 2024-03-31 18:25 ./usr/lib/s390x-linux-gnu/htslib/hfile_libcurl.so -rw-r--r-- root/root 38920 2024-03-31 18:25 ./usr/lib/s390x-linux-gnu/htslib/hfile_s3.so -rw-r--r-- root/root 22536 2024-03-31 18:25 ./usr/lib/s390x-linux-gnu/htslib/hfile_s3_write.so -rw-r--r-- root/root 981088 2024-03-31 18:25 ./usr/lib/s390x-linux-gnu/libhts.so.1.19 lrwxrwxrwx root/root 0 2024-03-31 18:25 ./usr/lib/s390x-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_s390x.deb --------------------------------- new Debian package, version 2.0. size 542634 bytes: control archive=1055 bytes. 1072 bytes, 21 lines control 478 bytes, 8 lines md5sums Package: tabix Source: htslib Version: 1.19+ds-1.1build3 Architecture: s390x Maintainer: Ubuntu Developers Installed-Size: 2604 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 755968 2024-03-31 18:25 ./usr/bin/bgzip -rwxr-xr-x root/root 911688 2024-03-31 18:25 ./usr/bin/htsfile -rwxr-xr-x root/root 932168 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: s390x Build Type: any Build-Space: 114960 Build-Time: 244 Distribution: noble-proposed Host Architecture: s390x Install-Time: 6 Job: htslib_1.19+ds-1.1build3.dsc Machine Architecture: s390x Package: htslib Package-Time: 252 Source-Version: 1.19+ds-1.1build3 Space: 114960 Status: successful Version: 1.19+ds-1.1build3 -------------------------------------------------------------------------------- Finished at 2024-03-31T21:47:15Z Build needed 00:04:12, 114960k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27988875 Scanning for processes to kill in build PACKAGEBUILD-27988875