https://launchpad.net/ubuntu/+source/python-pysam/0.22.1+ds-1/+build/28441281 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-017 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:46:06 UTC 2024 s390x Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 12 May 23:27:21 ntpdate[1895]: adjust time server 10.211.37.1 offset 0.000974 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=oracular --arch=s390x PACKAGEBUILD-28441281 --image-type chroot /home/buildd/filecache-default/c23f799bb684944311373fdcead5a58221fa6ef7 Creating target for build PACKAGEBUILD-28441281 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=oracular --arch=s390x PACKAGEBUILD-28441281 Starting target for build PACKAGEBUILD-28441281 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=oracular --arch=s390x PACKAGEBUILD-28441281 'deb http://ftpmaster.internal/ubuntu oracular main universe' 'deb http://ftpmaster.internal/ubuntu oracular-security main universe' 'deb http://ftpmaster.internal/ubuntu oracular-updates main universe' 'deb http://ftpmaster.internal/ubuntu oracular-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-28441281 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=oracular --arch=s390x PACKAGEBUILD-28441281 Updating target for build PACKAGEBUILD-28441281 Get:1 http://ftpmaster.internal/ubuntu oracular InRelease [73.9 kB] Get:2 http://ftpmaster.internal/ubuntu oracular-security InRelease [73.9 kB] Get:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease [73.9 kB] Get:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [73.9 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main s390x Packages [1322 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/universe s390x Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu oracular/universe Translation-en [6028 kB] Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x Packages [197 kB] Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main Translation-en [74.8 kB] Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x Packages [982 kB] Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe Translation-en [395 kB] Fetched 24.2 MB in 4s (5848 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 will be upgraded: advancecomp 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 findutils g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgmp10 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nis libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 172 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 108 MB of archives. After this operation, 78.1 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libtirpc-common all 1.3.4+ds-1.3 [8106 B] Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libtirpc-dev s390x 1.3.4+ds-1.3 [196 kB] Get:3 http://ftpmaster.internal/ubuntu oracular/main s390x libnsl-dev s390x 1.3.0-3build3 [73.1 kB] Get:4 http://ftpmaster.internal/ubuntu oracular/main s390x libnsl2 s390x 1.3.0-3build3 [44.1 kB] Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libtirpc3t64 s390x 1.3.4+ds-1.3 [84.9 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main s390x libgssapi-krb5-2 s390x 1.20.1-6ubuntu2 [149 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main s390x libkrb5-3 s390x 1.20.1-6ubuntu2 [360 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main s390x libk5crypto3 s390x 1.20.1-6ubuntu2 [90.3 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main s390x libkrb5support0 s390x 1.20.1-6ubuntu2 [34.7 kB] Get:10 http://ftpmaster.internal/ubuntu oracular/main s390x libargon2-1 s390x 0~20190702+dfsg-4build1 [54.1 kB] Get:11 http://ftpmaster.internal/ubuntu oracular/main s390x libblkid1 s390x 2.39.3-9ubuntu6 [128 kB] Get:12 http://ftpmaster.internal/ubuntu oracular/main s390x libpcre2-8-0 s390x 10.42-4ubuntu2 [245 kB] Get:13 http://ftpmaster.internal/ubuntu oracular/main s390x libselinux1 s390x 3.5-2ubuntu2 [84.8 kB] Get:14 http://ftpmaster.internal/ubuntu oracular/main s390x libcap2 s390x 1:2.66-5ubuntu2 [31.8 kB] Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libudev1 s390x 256~rc1-1~exp2ubuntu1 [191 kB] Get:16 http://ftpmaster.internal/ubuntu oracular/main s390x libdevmapper1.02.1 s390x 2:1.02.185-3ubuntu3 [142 kB] Get:17 http://ftpmaster.internal/ubuntu oracular/main s390x libjson-c5 s390x 0.17-1build1 [37.2 kB] Get:18 http://ftpmaster.internal/ubuntu oracular/main s390x libuuid1 s390x 2.39.3-9ubuntu6 [35.9 kB] Get:19 http://ftpmaster.internal/ubuntu oracular/main s390x libcryptsetup12 s390x 2:2.7.0-1ubuntu4 [264 kB] Get:20 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libacl1 s390x 2.3.2-2 [17.9 kB] Get:21 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libapparmor1 s390x 4.0.1-0ubuntu1 [51.4 kB] Get:22 http://ftpmaster.internal/ubuntu oracular/main s390x libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:23 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libcap-ng0 s390x 0.8.5-1 [15.7 kB] Get:24 http://ftpmaster.internal/ubuntu oracular/main s390x libaudit1 s390x 1:3.1.2-2.1build1 [48.9 kB] Get:25 http://ftpmaster.internal/ubuntu oracular/main s390x libcrypt-dev s390x 1:4.4.36-4build1 [119 kB] Get:26 http://ftpmaster.internal/ubuntu oracular/main s390x libcrypt1 s390x 1:4.4.36-4build1 [88.9 kB] Get:27 http://ftpmaster.internal/ubuntu oracular/main s390x libmount1 s390x 2.39.3-9ubuntu6 [138 kB] Get:28 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x perl-modules-5.38 all 5.38.2-4 [3110 kB] Get:29 http://ftpmaster.internal/ubuntu oracular/main s390x libdb5.3t64 s390x 5.3.28+dfsg2-7 [764 kB] Get:30 http://ftpmaster.internal/ubuntu oracular/main s390x libgdbm6t64 s390x 1.23-5.1build1 [36.5 kB] Get:31 http://ftpmaster.internal/ubuntu oracular/main s390x libgdbm-compat4t64 s390x 1.23-5.1build1 [6890 B] Get:32 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libperl5.38t64 s390x 5.38.2-4 [5025 kB] Get:33 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x perl s390x 5.38.2-4 [231 kB] Get:34 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x perl-base s390x 5.38.2-4 [1942 kB] Get:35 http://ftpmaster.internal/ubuntu oracular/main s390x liblocale-gettext-perl s390x 1.07-6ubuntu5 [15.8 kB] Get:36 http://ftpmaster.internal/ubuntu oracular/main s390x libtext-iconv-perl s390x 1.7-8build3 [13.8 kB] Get:37 http://ftpmaster.internal/ubuntu oracular/main s390x libtext-charwidth-perl s390x 0.04-11build3 [9518 B] Get:38 http://ftpmaster.internal/ubuntu oracular/universe s390x libnss-nisplus s390x 1.3-5build1 [23.8 kB] Get:39 http://ftpmaster.internal/ubuntu oracular/universe s390x libnss-nis s390x 3.1-0ubuntu7 [28.3 kB] Get:40 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc-dev-bin s390x 2.39-0ubuntu8.1 [20.2 kB] Get:41 http://ftpmaster.internal/ubuntu oracular/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu7 [66.4 kB] Get:42 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc6-dev s390x 2.39-0ubuntu8.1 [1629 kB] Get:43 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc6 s390x 2.39-0ubuntu8.1 [2847 kB] Get:44 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libc-bin s390x 2.39-0ubuntu8.1 [654 kB] Get:45 http://ftpmaster.internal/ubuntu oracular/main s390x openssl s390x 3.0.13-0ubuntu3 [1009 kB] Get:46 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libsystemd-shared s390x 256~rc1-1~exp2ubuntu1 [2232 kB] Get:47 http://ftpmaster.internal/ubuntu oracular/main s390x liblzma5 s390x 5.6.1+really5.4.5-1 [135 kB] Get:48 http://ftpmaster.internal/ubuntu oracular/main s390x libkmod2 s390x 31+20240202-2ubuntu7 [56.4 kB] Get:49 http://ftpmaster.internal/ubuntu oracular/main s390x libssl3t64 s390x 3.0.13-0ubuntu3 [1675 kB] Get:50 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x systemd-dev all 256~rc1-1~exp2ubuntu1 [105 kB] Get:51 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x systemd-sysv s390x 256~rc1-1~exp2ubuntu1 [11.9 kB] Get:52 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x systemd s390x 256~rc1-1~exp2ubuntu1 [3700 kB] Get:53 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libsystemd0 s390x 256~rc1-1~exp2ubuntu1 [449 kB] Get:54 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libapt-pkg6.0t64 s390x 2.9.2 [1009 kB] Get:55 http://ftpmaster.internal/ubuntu oracular/main s390x libnettle8t64 s390x 3.9.1-2.2build1 [210 kB] Get:56 http://ftpmaster.internal/ubuntu oracular/main s390x libhogweed6t64 s390x 3.9.1-2.2build1 [204 kB] Get:57 http://ftpmaster.internal/ubuntu oracular/main s390x libp11-kit0 s390x 0.25.3-4ubuntu2 [320 kB] Get:58 http://ftpmaster.internal/ubuntu oracular/main s390x libunistring5 s390x 1.2-1 [552 kB] Get:59 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libgnutls30t64 s390x 3.8.3-1.1ubuntu3.1 [944 kB] Get:60 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x apt s390x 2.9.2 [1417 kB] Get:61 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x apt-utils s390x 2.9.2 [219 kB] Get:62 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libpam-modules-bin s390x 1.5.3-7ubuntu1 [56.9 kB] Get:63 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libpam-modules s390x 1.5.3-7ubuntu1 [292 kB] Get:64 http://ftpmaster.internal/ubuntu oracular/main s390x bzip2 s390x 1.0.8-5.1 [35.5 kB] Get:65 http://ftpmaster.internal/ubuntu oracular/main s390x libbz2-1.0 s390x 1.0.8-5.1 [40.0 kB] Get:66 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x gcc-14-base s390x 14-20240429-1ubuntu1 [48.0 kB] Get:67 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libgcc-s1 s390x 14-20240429-1ubuntu1 [35.8 kB] Get:68 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libgpg-error-l10n all 1.49-2 [8228 B] Get:69 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libgpg-error0 s390x 1.49-2 [75.4 kB] Get:70 http://ftpmaster.internal/ubuntu oracular/main s390x libgcrypt20 s390x 1.10.3-2build1 [501 kB] Get:71 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x liblz4-1 s390x 1.9.4-2 [77.1 kB] Get:72 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libstdc++6 s390x 14-20240429-1ubuntu1 [905 kB] Get:73 http://ftpmaster.internal/ubuntu oracular/main s390x libxxhash0 s390x 0.8.2-2build1 [24.1 kB] Get:74 http://ftpmaster.internal/ubuntu oracular/main s390x libzstd1 s390x 1.5.5+dfsg2-2build1 [341 kB] Get:75 http://ftpmaster.internal/ubuntu oracular/main s390x zlib1g s390x 1:1.3.dfsg-3.1ubuntu2 [75.9 kB] Get:76 http://ftpmaster.internal/ubuntu oracular/main s390x libgmp10 s390x 2:6.3.0+dfsg-2ubuntu6 [337 kB] Get:77 http://ftpmaster.internal/ubuntu oracular/main s390x libffi8 s390x 3.4.6-1build1 [23.1 kB] Get:78 http://ftpmaster.internal/ubuntu oracular/main s390x libidn2-0 s390x 2.3.7-2build1 [67.3 kB] Get:79 http://ftpmaster.internal/ubuntu oracular/main s390x libtasn1-6 s390x 4.19.0-3build1 [48.5 kB] Get:80 http://ftpmaster.internal/ubuntu oracular/main s390x libdebconfclient0 s390x 0.271ubuntu3 [11.4 kB] Get:81 http://ftpmaster.internal/ubuntu oracular/main s390x base-passwd s390x 3.6.3build1 [51.5 kB] Get:82 http://ftpmaster.internal/ubuntu oracular/main s390x libassuan0 s390x 2.5.6-1build1 [38.3 kB] Get:83 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libsqlite3-0 s390x 3.45.3-1 [735 kB] Get:84 http://ftpmaster.internal/ubuntu oracular/main s390x gpg s390x 2.4.4-2ubuntu17 [589 kB] Get:85 http://ftpmaster.internal/ubuntu oracular/main s390x libreadline8t64 s390x 8.2-4build1 [171 kB] Get:86 http://ftpmaster.internal/ubuntu oracular/main s390x readline-common all 8.2-4build1 [56.5 kB] Get:87 http://ftpmaster.internal/ubuntu oracular/main s390x libncursesw6 s390x 6.4+20240113-1ubuntu2 [161 kB] Get:88 http://ftpmaster.internal/ubuntu oracular/main s390x libtinfo6 s390x 6.4+20240113-1ubuntu2 [117 kB] Get:89 http://ftpmaster.internal/ubuntu oracular/main s390x gpg-agent s390x 2.4.4-2ubuntu17 [240 kB] Get:90 http://ftpmaster.internal/ubuntu oracular/main s390x gpgconf s390x 2.4.4-2ubuntu17 [111 kB] Get:91 http://ftpmaster.internal/ubuntu oracular/main s390x pinentry-curses s390x 1.2.1-3ubuntu5 [37.6 kB] Get:92 http://ftpmaster.internal/ubuntu oracular/main s390x init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:93 http://ftpmaster.internal/ubuntu oracular/main s390x libnpth0t64 s390x 1.6-3.1build1 [8204 B] Get:94 http://ftpmaster.internal/ubuntu oracular/main s390x gpgv s390x 2.4.4-2ubuntu17 [165 kB] Get:95 http://ftpmaster.internal/ubuntu oracular/main s390x ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:96 http://ftpmaster.internal/ubuntu oracular/main s390x libseccomp2 s390x 2.5.5-1ubuntu3 [53.4 kB] Get:97 http://ftpmaster.internal/ubuntu oracular/main s390x debconf-i18n all 1.5.86ubuntu1 [205 kB] Get:98 http://ftpmaster.internal/ubuntu oracular/main s390x debconf all 1.5.86ubuntu1 [124 kB] Get:99 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libpam0g s390x 1.5.3-7ubuntu1 [69.8 kB] Get:100 http://ftpmaster.internal/ubuntu oracular/main s390x libfdisk1 s390x 2.39.3-9ubuntu6 [151 kB] Get:101 http://ftpmaster.internal/ubuntu oracular/main s390x mount s390x 2.39.3-9ubuntu6 [119 kB] Get:102 http://ftpmaster.internal/ubuntu oracular/main s390x libcom-err2 s390x 1.47.0-2.4~exp1ubuntu4 [22.9 kB] Get:103 http://ftpmaster.internal/ubuntu oracular/main s390x libkeyutils1 s390x 1.6.3-3build1 [9556 B] Get:104 http://ftpmaster.internal/ubuntu oracular/main s390x linux-libc-dev s390x 6.8.0-31.31 [1593 kB] Get:105 http://ftpmaster.internal/ubuntu oracular/main s390x base-files s390x 13.1ubuntu1 [73.8 kB] Get:106 http://ftpmaster.internal/ubuntu oracular/main s390x debianutils s390x 5.17build1 [90.2 kB] Get:107 http://ftpmaster.internal/ubuntu oracular/main s390x bash s390x 5.2.21-2ubuntu4 [845 kB] Get:108 http://ftpmaster.internal/ubuntu oracular/main s390x bsdutils s390x 1:2.39.3-9ubuntu6 [96.5 kB] Get:109 http://ftpmaster.internal/ubuntu oracular/main s390x coreutils s390x 9.4-3ubuntu6 [1483 kB] Get:110 http://ftpmaster.internal/ubuntu oracular/main s390x tar s390x 1.35+dfsg-3build1 [269 kB] Get:111 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x dpkg s390x 1.22.6ubuntu10 [1274 kB] Get:112 http://ftpmaster.internal/ubuntu oracular/main s390x dash s390x 0.5.12-6ubuntu5 [95.0 kB] Get:113 http://ftpmaster.internal/ubuntu oracular/main s390x diffutils s390x 1:3.10-1build1 [188 kB] Get:114 http://ftpmaster.internal/ubuntu oracular/main s390x findutils s390x 4.9.0-5build1 [305 kB] Get:115 http://ftpmaster.internal/ubuntu oracular/main s390x grep s390x 3.11-4build1 [173 kB] Get:116 http://ftpmaster.internal/ubuntu oracular/main s390x gzip s390x 1.12-1ubuntu3 [107 kB] Get:117 http://ftpmaster.internal/ubuntu oracular/main s390x hostname s390x 3.23+nmu2ubuntu2 [11.2 kB] Get:118 http://ftpmaster.internal/ubuntu oracular/main s390x login s390x 1:4.13+dfsg1-4ubuntu3 [202 kB] Get:119 http://ftpmaster.internal/ubuntu oracular/main s390x ncurses-bin s390x 6.4+20240113-1ubuntu2 [198 kB] Get:120 http://ftpmaster.internal/ubuntu oracular/main s390x sed s390x 4.9-2build1 [198 kB] Get:121 http://ftpmaster.internal/ubuntu oracular/main s390x util-linux s390x 2.39.3-9ubuntu6 [1142 kB] Get:122 http://ftpmaster.internal/ubuntu oracular/main s390x ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] Get:123 http://ftpmaster.internal/ubuntu oracular/main s390x sysvinit-utils s390x 3.08-6ubuntu3 [34.8 kB] Get:124 http://ftpmaster.internal/ubuntu oracular/main s390x logsave s390x 1.47.0-2.4~exp1ubuntu4 [22.6 kB] Get:125 http://ftpmaster.internal/ubuntu oracular/main s390x libext2fs2t64 s390x 1.47.0-2.4~exp1ubuntu4 [234 kB] Get:126 http://ftpmaster.internal/ubuntu oracular/main s390x e2fsprogs s390x 1.47.0-2.4~exp1ubuntu4 [614 kB] Get:127 http://ftpmaster.internal/ubuntu oracular/main s390x optipng s390x 0.7.8+ds-1build2 [114 kB] Get:128 http://ftpmaster.internal/ubuntu oracular/main s390x libpng16-16t64 s390x 1.6.43-5build1 [200 kB] Get:129 http://ftpmaster.internal/ubuntu oracular/main s390x init s390x 1.66ubuntu1 [6188 B] Get:130 http://ftpmaster.internal/ubuntu oracular/main s390x libsmartcols1 s390x 2.39.3-9ubuntu6 [68.2 kB] Get:131 http://ftpmaster.internal/ubuntu oracular/main s390x uuid-runtime s390x 2.39.3-9ubuntu6 [33.4 kB] Get:132 http://ftpmaster.internal/ubuntu oracular/main s390x libattr1 s390x 1:2.5.2-1build1 [11.7 kB] Get:133 http://ftpmaster.internal/ubuntu oracular/main s390x libmd0 s390x 1.1.0-2build1 [24.6 kB] Get:134 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libpam-runtime all 1.5.3-7ubuntu1 [40.8 kB] Get:135 http://ftpmaster.internal/ubuntu oracular/main s390x libsemanage-common all 3.5-1build5 [10.1 kB] Get:136 http://ftpmaster.internal/ubuntu oracular/main s390x libsepol2 s390x 3.5-2build1 [315 kB] Get:137 http://ftpmaster.internal/ubuntu oracular/main s390x libsemanage2 s390x 3.5-1build5 [96.8 kB] Get:138 http://ftpmaster.internal/ubuntu oracular/main s390x passwd s390x 1:4.13+dfsg1-4ubuntu3 [857 kB] Get:139 http://ftpmaster.internal/ubuntu oracular/main s390x libproc2-0 s390x 2:4.0.4-4ubuntu3 [59.8 kB] Get:140 http://ftpmaster.internal/ubuntu oracular/main s390x libss2 s390x 1.47.0-2.4~exp1ubuntu4 [17.2 kB] Get:141 http://ftpmaster.internal/ubuntu oracular/main s390x mawk s390x 1.3.4.20240123-1build1 [133 kB] Get:142 http://ftpmaster.internal/ubuntu oracular/main s390x procps s390x 2:4.0.4-4ubuntu3 [724 kB] Get:143 http://ftpmaster.internal/ubuntu oracular/main s390x sensible-utils all 0.0.22 [22.5 kB] Get:144 http://ftpmaster.internal/ubuntu oracular/main s390x ca-certificates all 20240203 [159 kB] Get:145 http://ftpmaster.internal/ubuntu oracular/main s390x krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:146 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x tzdata all 2024a-4ubuntu1 [274 kB] Get:147 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x bash-completion all 1:2.13.0-1 [205 kB] Get:148 http://ftpmaster.internal/ubuntu oracular/main s390x bsdextrautils s390x 2.39.3-9ubuntu6 [76.3 kB] Get:149 http://ftpmaster.internal/ubuntu oracular/main s390x libgpm2 s390x 1.20.7-11 [14.7 kB] Get:150 http://ftpmaster.internal/ubuntu oracular/main s390x libip4tc2 s390x 1.8.10-3ubuntu2 [24.2 kB] Get:151 http://ftpmaster.internal/ubuntu oracular/main s390x libjansson4 s390x 2.14-2build2 [33.2 kB] Get:152 http://ftpmaster.internal/ubuntu oracular/main s390x psmisc s390x 23.7-1build1 [178 kB] Get:153 http://ftpmaster.internal/ubuntu oracular/main s390x xz-utils s390x 5.6.1+really5.4.5-1 [269 kB] Get:154 http://ftpmaster.internal/ubuntu oracular/main s390x advancecomp s390x 2.5-1build1 [205 kB] Get:155 http://ftpmaster.internal/ubuntu oracular/main s390x libctf0 s390x 2.42-4ubuntu2 [98.4 kB] Get:156 http://ftpmaster.internal/ubuntu oracular/main s390x libctf-nobfd0 s390x 2.42-4ubuntu2 [100 kB] Get:157 http://ftpmaster.internal/ubuntu oracular/main s390x binutils-s390x-linux-gnu s390x 2.42-4ubuntu2 [2270 kB] Get:158 http://ftpmaster.internal/ubuntu oracular/main s390x libbinutils s390x 2.42-4ubuntu2 [479 kB] Get:159 http://ftpmaster.internal/ubuntu oracular/main s390x binutils s390x 2.42-4ubuntu2 [3042 B] Get:160 http://ftpmaster.internal/ubuntu oracular/main s390x binutils-common s390x 2.42-4ubuntu2 [217 kB] Get:161 http://ftpmaster.internal/ubuntu oracular/main s390x libsframe1 s390x 2.42-4ubuntu2 [14.2 kB] Get:162 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libubsan1 s390x 14-20240429-1ubuntu1 [1189 kB] Get:163 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libgomp1 s390x 14-20240429-1ubuntu1 [151 kB] Get:164 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libitm1 s390x 14-20240429-1ubuntu1 [31.1 kB] Get:165 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libatomic1 s390x 14-20240429-1ubuntu1 [9394 B] Get:166 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libasan8 s390x 14-20240429-1ubuntu1 [3004 kB] Get:167 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x g++-13 s390x 13.2.0-24ubuntu1 [15.0 kB] Get:168 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x gcc-13 s390x 13.2.0-24ubuntu1 [474 kB] Get:169 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libstdc++-13-dev s390x 13.2.0-24ubuntu1 [2495 kB] Get:170 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libgcc-13-dev s390x 13.2.0-24ubuntu1 [1003 kB] Get:171 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libcc1-0 s390x 14-20240429-1ubuntu1 [50.0 kB] Get:172 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x cpp-13 s390x 13.2.0-24ubuntu1 [1030 B] Get:173 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x gcc-13-base s390x 13.2.0-24ubuntu1 [49.3 kB] Get:174 http://ftpmaster.internal/ubuntu oracular/main s390x libisl23 s390x 0.26-3build1 [713 kB] Get:175 http://ftpmaster.internal/ubuntu oracular/main s390x libmpfr6 s390x 4.2.1-1build1 [322 kB] Get:176 http://ftpmaster.internal/ubuntu oracular/main s390x libmpc3 s390x 1.3.1-1build1 [58.4 kB] Get:177 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x gcc-13-s390x-linux-gnu s390x 13.2.0-24ubuntu1 [19.1 MB] Get:178 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x g++-13-s390x-linux-gnu s390x 13.2.0-24ubuntu1 [11.3 MB] Get:179 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x cpp-13-s390x-linux-gnu s390x 13.2.0-24ubuntu1 [9936 kB] Get:180 http://ftpmaster.internal/ubuntu oracular/main s390x g++ s390x 4:13.2.0-7ubuntu1 [1096 B] Get:181 http://ftpmaster.internal/ubuntu oracular/main s390x gcc s390x 4:13.2.0-7ubuntu1 [5014 B] Get:182 http://ftpmaster.internal/ubuntu oracular/main s390x cpp s390x 4:13.2.0-7ubuntu1 [22.4 kB] Get:183 http://ftpmaster.internal/ubuntu oracular/main s390x cpp-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [5308 B] Get:184 http://ftpmaster.internal/ubuntu oracular/main s390x gcc-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [1208 B] Get:185 http://ftpmaster.internal/ubuntu oracular/main s390x g++-s390x-linux-gnu s390x 4:13.2.0-7ubuntu1 [956 B] Get:186 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x dpkg-dev all 1.22.6ubuntu10 [1074 kB] Get:187 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libdpkg-perl all 1.22.6ubuntu10 [269 kB] Get:188 http://ftpmaster.internal/ubuntu oracular/main s390x patch s390x 2.7.6-7build3 [113 kB] Get:189 http://ftpmaster.internal/ubuntu oracular/main s390x make s390x 4.3-4.1build2 [196 kB] Get:190 http://ftpmaster.internal/ubuntu oracular/main s390x lto-disabled-list all 48 [12.3 kB] Get:191 http://ftpmaster.internal/ubuntu oracular/main s390x libfakeroot s390x 1.34-1 [31.9 kB] Get:192 http://ftpmaster.internal/ubuntu oracular/main s390x fakeroot s390x 1.34-1 [67.4 kB] Get:193 http://ftpmaster.internal/ubuntu oracular/main s390x liblockfile-bin s390x 1.17-1build3 [11.6 kB] Get:194 http://ftpmaster.internal/ubuntu oracular/main s390x liblockfile1 s390x 1.17-1build3 [7028 B] Get:195 http://ftpmaster.internal/ubuntu oracular/main s390x lockfile-progs s390x 0.1.19+nmu1 [8720 B] Preconfiguring packages ... Fetched 108 MB in 9s (12.0 MB/s) (Reading database ... 13395 files and directories currently installed.) Preparing to unpack .../libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) over (1.3.3+ds-1) ... Preparing to unpack .../libtirpc-dev_1.3.4+ds-1.3_s390x.deb ... Unpacking libtirpc-dev:s390x (1.3.4+ds-1.3) over (1.3.3+ds-1) ... Preparing to unpack .../libnsl-dev_1.3.0-3build3_s390x.deb ... Unpacking libnsl-dev:s390x (1.3.0-3build3) over (1.3.0-2build2) ... Preparing to unpack .../libnsl2_1.3.0-3build3_s390x.deb ... Unpacking libnsl2:s390x (1.3.0-3build3) over (1.3.0-2build2) ... dpkg: libtirpc3:s390x: dependency problems, but removing anyway as you requested: libnss-nisplus:s390x depends on libtirpc3 (>= 1.0.2). (Reading database ... 13395 files and directories currently installed.) Removing libtirpc3:s390x (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3t64:s390x. 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Setting up libdb5.3t64:s390x (5.3.28+dfsg2-7) ... 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 ... 14813 files and directories currently installed.) Removing libgdbm6:s390x (1.23-3) ... Selecting previously unselected package libgdbm6t64:s390x. (Reading database ... 14808 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 ... 14814 files and directories currently installed.) Removing libgdbm-compat4:s390x (1.23-3) ... Selecting previously unselected package libgdbm-compat4t64:s390x. (Reading database ... 14809 files and directories currently installed.) 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(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 ... 15538 files and directories currently installed.) Preparing to unpack .../gcc-14-base_14-20240429-1ubuntu1_s390x.deb ... Unpacking gcc-14-base:s390x (14-20240429-1ubuntu1) ... Setting up gcc-14-base:s390x (14-20240429-1ubuntu1) ... 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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+20240113-1ubuntu2_s390x.deb ... Unpacking libncursesw6:s390x (6.4+20240113-1ubuntu2) over (6.4+20230625-2) ... Preparing to unpack .../libtinfo6_6.4+20240113-1ubuntu2_s390x.deb ... 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Setting up rpcsvc-proto (1.4.2-0ubuntu7) ... Setting up gcc-13-base:s390x (13.2.0-24ubuntu1) ... Setting up make (4.3-4.1build2) ... Setting up libmpfr6:s390x (4.2.1-1build1) ... Setting up bash-completion (1:2.13.0-1) ... Installing new version of config file /etc/profile.d/bash_completion.sh ... Setting up xz-utils (5.6.1+really5.4.5-1) ... Setting up perl-modules-5.38 (5.38.2-4) ... Setting up libproc2-0:s390x (2:4.0.4-4ubuntu3) ... Setting up libpng16-16t64:s390x (1.6.43-5build1) ... Setting up libmpc3:s390x (1.3.1-1build1) ... Setting up libatomic1:s390x (14-20240429-1ubuntu1) ... Setting up patch (2.7.6-7build3) ... Setting up libss2:s390x (1.47.0-2.4~exp1ubuntu4) ... Setting up libncursesw6:s390x (6.4+20240113-1ubuntu2) ... Setting up libk5crypto3:s390x (1.20.1-6ubuntu2) ... Setting up logsave (1.47.0-2.4~exp1ubuntu4) ... Setting up libubsan1:s390x (14-20240429-1ubuntu1) ... Setting up advancecomp (2.5-1build1) ... Setting up sensible-utils (0.0.22) ... Setting up uuid-runtime (2.39.3-9ubuntu6) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libcrypt-dev:s390x (1:4.4.36-4build1) ... Setting up libasan8:s390x (14-20240429-1ubuntu1) ... Setting up procps (2:4.0.4-4ubuntu3) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1build1) ... Setting up libkrb5-3:s390x (1.20.1-6ubuntu2) ... Setting up liblockfile1:s390x (1.17-1build3) ... Setting up libperl5.38t64:s390x (5.38.2-4) ... Setting up libbinutils:s390x (2.42-4ubuntu2) ... Setting up libisl23:s390x (0.26-3build1) ... Setting up libc-dev-bin (2.39-0ubuntu8.1) ... Setting up openssl (3.0.13-0ubuntu3) ... Setting up libgpg-error-l10n (1.49-2) ... Setting up readline-common (8.2-4build1) ... Setting up libcc1-0:s390x (14-20240429-1ubuntu1) ... Setting up liblocale-gettext-perl (1.07-6ubuntu5) ... Setting up libitm1:s390x (14-20240429-1ubuntu1) ... Setting up libkmod2:s390x (31+20240202-2ubuntu7) ... Setting up libctf0:s390x (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up binutils-s390x-linux-gnu (2.42-4ubuntu2) ... Setting up debconf-i18n (1.5.86ubuntu1) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... 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 (5.38.2-4) ... Setting up cpp-13-s390x-linux-gnu (13.2.0-24ubuntu1) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19+nmu1) ... Setting up libgssapi-krb5-2:s390x (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu10) ... Setting up libreadline8t64:s390x (8.2-4build1) ... Setting up libgcc-13-dev:s390x (13.2.0-24ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:s390x (2.39-0ubuntu8.1) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up libstdc++-13-dev:s390x (13.2.0-24ubuntu1) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up cpp-13 (13.2.0-24ubuntu1) ... Setting up cpp-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libtirpc3t64:s390x (1.3.4+ds-1.3) ... Setting up dpkg-dev (1.22.6ubuntu10) ... Setting up libtirpc-dev:s390x (1.3.4+ds-1.3) ... Setting up gcc-13-s390x-linux-gnu (13.2.0-24ubuntu1) ... Setting up gcc-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13-s390x-linux-gnu (13.2.0-24ubuntu1) ... Setting up gcc-13 (13.2.0-24ubuntu1) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:s390x (1.3.0-3build3) ... Setting up g++-13 (13.2.0-24ubuntu1) ... Setting up g++-s390x-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:s390x (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnss-nis:s390x (3.1-0ubuntu7) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:s390x (1.3.0-3build3) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15763 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-28441281 s390x oracular-proposed -c chroot:build-PACKAGEBUILD-28441281 --arch=s390x --dist=oracular-proposed --nolog python-pysam_0.22.1+ds-1.dsc Initiating build PACKAGEBUILD-28441281 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:46:06 UTC 2024 s390x sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-s390x-017.buildd +==============================================================================+ | python-pysam 0.22.1+ds-1 (s390x) Sun, 12 May 2024 23:28:04 +0000 | +==============================================================================+ Package: python-pysam Version: 0.22.1+ds-1 Source Version: 0.22.1+ds-1 Distribution: oracular-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28441281/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-JelgJy/resolver-4WIiK9' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.22.1+ds-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-pysam-JelgJy/python-pysam-0.22.1+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-JelgJy' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, libhts-dev (>= 1.14~), zlib1g-dev, python3-all-dev, python3-setuptools, cython3, tabix, samtools, bcftools, python3-pytest, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, libhts-dev (>= 1.14~), zlib1g-dev, python3-all-dev, python3-setuptools, cython3, tabix, samtools, bcftools, python3-pytest, 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 [456 B] Get:5 copy:/<>/apt_archive ./ Packages [527 B] Fetched 1940 B in 0s (104 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 libkmod2 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 bcftools blt cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcairo2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgraphite2-3 libharfbuzz0b libhts-dev libhts3t64 libhtscodecs2 libicu74 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libopenjp2-7 libpipeline1 libpixman-1-0 libpsl5t64 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libssh-4 libsub-override-perl libtcl8.6 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 m4 man-db media-types netbase po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-argcomplete python3-argh python3-attr python3-biopython python3-brotli python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-fonttools python3-freetype python3-fs python3-gffutils python3-importlib-metadata python3-iniconfig python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy python3-pyfaidx python3-pyparsing python3-pytest python3-reportlab python3-rlpycairo python3-scipy python3-setuptools python3-simplejson python3-six python3-sympy python3-tk python3-tz python3-ufolib2 python3-zipp python3.12 python3.12-dev python3.12-minimal samtools sgml-base tabix tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc texlive-latex-recommended blt-demo cython-doc dh-make flit python3-build python3-installer python3-wheel fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config low-memory-monitor libjs-jquery-ui-docs liblcms2-utils liblzma-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee wise python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gfortran python-pil-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python-setuptools-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.12-venv python3.12-doc binfmt-support cwltool sgml-base-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+ python3-pybedtools python3-bs4 python3-cssselect python3-html5lib python3-olefile python3-pygments fonts-dejavu-extra isympy-common The following NEW packages will be installed: autoconf automake autopoint autotools-dev bcftools blt cython3 debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx fonts-urw-base35 gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcairo2 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgraphite2-3 libharfbuzz0b libhts-dev libhts3t64 libhtscodecs2 libicu74 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libldap2 liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libopenjp2-7 libpipeline1 libpixman-1-0 libpsl5t64 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libraqm0 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libssh-4 libsub-override-perl libtcl8.6 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 m4 man-db media-types netbase po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-argcomplete python3-argh python3-attr python3-biopython python3-brotli python3-cairo python3-chardet python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-fonttools python3-freetype python3-fs python3-gffutils python3-importlib-metadata python3-iniconfig python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy python3-pyfaidx python3-pyparsing python3-pytest python3-reportlab python3-rlpycairo python3-scipy python3-setuptools python3-simplejson python3-six python3-sympy python3-tk python3-tz python3-ufolib2 python3-zipp python3.12 python3.12-dev python3.12-minimal samtools sbuild-build-depends-main-dummy sgml-base tabix tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core zlib1g-dev 0 upgraded, 177 newly installed, 0 to remove and 0 not upgraded. Need to get 128 MB of archives. After this operation, 480 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [746 B] Get:2 http://ftpmaster.internal/ubuntu oracular/main s390x libpython3.12-minimal s390x 3.12.3-1 [830 kB] Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libexpat1 s390x 2.6.2-1 [91.6 kB] Get:4 http://ftpmaster.internal/ubuntu oracular/main s390x python3.12-minimal s390x 3.12.3-1 [2460 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main s390x python3-minimal s390x 3.12.3-0ubuntu1 [27.2 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main s390x media-types all 10.1.0 [27.5 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main s390x netbase all 6.4 [13.1 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main s390x libpython3.12-stdlib s390x 3.12.3-1 [2066 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main s390x python3.12 s390x 3.12.3-1 [651 kB] Get:10 http://ftpmaster.internal/ubuntu oracular/main s390x libpython3-stdlib s390x 3.12.3-0ubuntu1 [9898 B] Get:11 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1.20-1 [45.8 kB] Get:50 http://ftpmaster.internal/ubuntu oracular/universe s390x libhtscodecs2 s390x 1.6.0-1build1 [87.0 kB] Get:51 http://ftpmaster.internal/ubuntu oracular/universe s390x libhts3t64 s390x 1.19+ds-1.1build3 [474 kB] Get:52 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x python3-argcomplete all 3.3.0-1 [34.5 kB] Get:53 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-argh all 0.31.2-1 [26.9 kB] Get:54 http://ftpmaster.internal/ubuntu oracular/main s390x python3-more-itertools all 10.2.0-1 [52.9 kB] Get:55 http://ftpmaster.internal/ubuntu oracular/main s390x python3-zipp all 1.0.0-6 [6090 B] Get:56 http://ftpmaster.internal/ubuntu oracular/main s390x python3-importlib-metadata all 4.12.0-1 [17.8 kB] Get:57 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x python3-pyfaidx all 0.8.1.1-2 [29.6 kB] Get:58 http://ftpmaster.internal/ubuntu oracular/main s390x python3-simplejson s390x 3.19.2-1build2 [55.2 kB] Get:59 http://ftpmaster.internal/ubuntu oracular/main s390x libblas3 s390x 3.12.0-3build1 [245 kB] Get:60 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libgfortran5 s390x 14-20240429-1ubuntu1 [600 kB] Get:61 http://ftpmaster.internal/ubuntu oracular/main s390x liblapack3 s390x 3.12.0-3build1 [2976 kB] Get:62 http://ftpmaster.internal/ubuntu oracular/main s390x python3-numpy s390x 1:1.26.4+ds-6ubuntu1 [4119 kB] Get:63 http://ftpmaster.internal/ubuntu oracular/main s390x python3-chardet all 5.2.0+dfsg-1 [117 kB] Get:64 http://ftpmaster.internal/ubuntu oracular/main s390x libtcl8.6 s390x 8.6.14+dfsg-1build1 [1038 kB] Get:65 http://ftpmaster.internal/ubuntu oracular/main s390x libfreetype6 s390x 2.13.2+dfsg-1build3 [437 kB] Get:66 http://ftpmaster.internal/ubuntu oracular/main s390x fonts-dejavu-mono all 2.37-8 [502 kB] Get:67 http://ftpmaster.internal/ubuntu oracular/main s390x fonts-dejavu-core all 2.37-8 [835 kB] Get:68 http://ftpmaster.internal/ubuntu oracular/main s390x libfontenc1 s390x 1:1.1.8-1build1 [14.8 kB] Get:69 http://ftpmaster.internal/ubuntu oracular/main s390x x11-common all 1:7.7+23ubuntu3 [21.7 kB] Get:70 http://ftpmaster.internal/ubuntu oracular/main s390x xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB] Get:71 http://ftpmaster.internal/ubuntu oracular/main s390x xfonts-utils s390x 1:7.7+6build3 [99.3 kB] Get:72 http://ftpmaster.internal/ubuntu oracular/main s390x fonts-urw-base35 all 20200910-8 [11.0 MB] Get:73 http://ftpmaster.internal/ubuntu oracular/main s390x fontconfig-config s390x 2.15.0-1.1ubuntu2 [37.4 kB] Get:74 http://ftpmaster.internal/ubuntu oracular/main s390x libfontconfig1 s390x 2.15.0-1.1ubuntu2 [150 kB] Get:75 http://ftpmaster.internal/ubuntu oracular/main s390x libxrender1 s390x 1:0.9.10-1.1build1 [20.4 kB] Get:76 http://ftpmaster.internal/ubuntu oracular/main s390x libxft2 s390x 2.3.6-1build1 [49.6 kB] Get:77 http://ftpmaster.internal/ubuntu oracular/main s390x libxss1 s390x 1:1.2.3-1build3 [7396 B] Get:78 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libopenjp2-7 s390x 2.5.0-2build3 [192 kB] Get:88 http://ftpmaster.internal/ubuntu oracular/main s390x libgraphite2-3 s390x 1.3.14-2build1 [80.0 kB] Get:89 http://ftpmaster.internal/ubuntu oracular/main s390x libharfbuzz0b s390x 8.3.0-2build2 [515 kB] Get:90 http://ftpmaster.internal/ubuntu oracular/main s390x libraqm0 s390x 0.10.1-1build1 [16.2 kB] Get:91 http://ftpmaster.internal/ubuntu oracular/main s390x libjbig0 s390x 2.1-6.1ubuntu2 [33.1 kB] Get:92 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libsharpyuv0 s390x 1.4.0-0.1 [16.2 kB] Get:93 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libwebp7 s390x 1.4.0-0.1 [204 kB] Get:94 http://ftpmaster.internal/ubuntu oracular/main s390x libtiff6 s390x 4.5.1+git230720-4ubuntu2 [218 kB] Get:95 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libwebpdemux2 s390x 1.4.0-0.1 [12.2 kB] Get:96 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x libwebpmux3 s390x 1.4.0-0.1 [25.3 kB] Get:97 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xml-core all 0.19 [20.3 kB] Get:107 http://ftpmaster.internal/ubuntu oracular/universe s390x w3c-sgml-lib all 1.3-3 [280 kB] Get:108 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x python3-biopython s390x 1.83+dfsg1-2 [1679 kB] Get:109 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-gffutils all 0.13-1 [1081 kB] Get:110 http://ftpmaster.internal/ubuntu oracular/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:111 http://ftpmaster.internal/ubuntu oracular/universe s390x libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] Get:112 http://ftpmaster.internal/ubuntu oracular/universe s390x fonts-lyx all 2.4.0~RC4-1 [170 kB] Get:113 http://ftpmaster.internal/ubuntu oracular/universe s390x python-matplotlib-data all 3.6.3-1ubuntu5 [2936 kB] Get:114 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x python3-six all 1.16.0-6 [13.0 kB] Get:115 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x python3-dateutil all 2.9.0-2 [80.3 kB] 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s390x 3.12.3-0ubuntu1 [914 B] Get:173 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] Get:174 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x python3-pluggy all 1.5.0-1 [21.0 kB] Get:175 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x python3-pytest all 8.1.2-1 [248 kB] Get:176 http://ftpmaster.internal/ubuntu oracular/universe s390x samtools s390x 1.19.2-1build2 [612 kB] Get:177 http://ftpmaster.internal/ubuntu oracular/universe s390x tabix s390x 1.19+ds-1.1build3 [543 kB] Preconfiguring packages ... Fetched 128 MB in 25s (5126 kB/s) Selecting previously unselected package libpython3.12-minimal:s390x. (Reading database ... 15763 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.3-1_s390x.deb ... Unpacking libpython3.12-minimal:s390x (3.12.3-1) ... Selecting previously unselected package libexpat1:s390x. Preparing to unpack .../libexpat1_2.6.2-1_s390x.deb ... Unpacking libexpat1:s390x (2.6.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.3-1_s390x.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Setting up libpython3.12-minimal:s390x (3.12.3-1) ... Setting up libexpat1:s390x (2.6.2-1) ... Setting up python3.12-minimal (3.12.3-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 16081 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.3-0ubuntu1_s390x.deb ... 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Setting up libpixman-1-0:s390x (0.42.2-1build1) ... Setting up libsharpyuv0:s390x (1.4.0-0.1) ... Setting up libxau6:s390x (1:1.0.9-1build6) ... Setting up libmagic-mgc (1:5.45-3build1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up fonts-lyx (2.4.0~RC4-1) ... Setting up libdebhelper-perl (13.14.1ubuntu5) ... Setting up libbrotli1:s390x (1.1.0-2build2) ... Setting up libmagic1t64:s390x (1:5.45-3build1) ... Setting up x11-common (1:7.7+23ubuntu3) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libpsl5t64:s390x (0.21.2-1.1build1) ... Setting up libnghttp2-14:s390x (1.61.0-1) ... Setting up libdeflate0:s390x (1.20-1) ... Setting up gettext-base (0.21-14ubuntu2) ... Setting up m4 (1.4.19-4build1) ... Setting up libqhull-r8.0:s390x (2020.2-6build1) ... Setting up file (1:5.45-3build1) ... Setting up libjbig0:s390x (2.1-6.1ubuntu2) ... Setting up libelf1t64:s390x (0.191-1) ... Setting up libdw1t64:s390x (0.191-1) ... Setting up libsasl2-modules-db:s390x (2.1.28+dfsg1-5ubuntu3) ... Setting up unicode-data (15.1.0-1) ... Setting up libfontenc1:s390x (1:1.1.8-1build1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:s390x (2.80.1-0ubuntu2) ... No schema files found: doing nothing. Setting up libblas3:s390x (3.12.0-3build1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode Setting up libexpat1-dev:s390x (2.6.2-1) ... Setting up libfreetype6:s390x (2.13.2+dfsg-1build3) ... Setting up libx11-data (2:1.8.7-1build1) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build7) ... Setting up libncurses6:s390x (6.4+20240113-1ubuntu2) ... Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... Setting up libfribidi0:s390x (1.0.13-3build1) ... Setting up libimagequant0:s390x (2.18.0-1build1) ... Setting up fonts-dejavu-mono (2.37-8) ... 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Setting up python-matplotlib-data (3.6.3-1ubuntu5) ... Setting up libwebpmux3:s390x (1.4.0-0.1) ... Setting up libbsd0:s390x (0.12.2-1) ... Setting up libdeflate-dev:s390x (1.20-1) ... Setting up tabix (1.19+ds-1.1build3) ... Setting up libxml2:s390x (2.9.14+dfsg-1.3ubuntu3) ... Setting up libldap2:s390x (2.6.7+dfsg-1~exp1ubuntu8) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libjpeg8:s390x (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:s390x (1:1.1.3-0ubuntu6) ... Setting up liblapack3:s390x (3.12.0-3build1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode Setting up libxcb1:s390x (1.15-1ubuntu2) ... 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Setting up libxslt1.1:s390x (1.1.39-0exp1build1) ... Setting up libhts3t64:s390x (1.19+ds-1.1build3) ... Setting up libx11-6:s390x (2:1.8.7-1build1) ... Setting up libfontconfig1:s390x (2.15.0-1.1ubuntu2) ... Setting up libpython3-stdlib:s390x (3.12.3-0ubuntu1) ... Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... Setting up libxrender1:s390x (1:0.9.10-1.1build1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:s390x (2:1.3.4-1build2) ... Setting up libhts-dev:s390x (1.19+ds-1.1build3) ... Setting up python3 (3.12.3-0ubuntu1) ... Setting up libpython3.12-dev:s390x (3.12.3-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' → '/usr/lib/systemd/system/man-db.timer'. Setting up libcairo2:s390x (1.18.0-3build1) ... Setting up python3-tz (2024.1-2) ... Setting up samtools (1.19.2-1build2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-simplejson (3.19.2-1build2) ... Setting up python3-pil:s390x (10.2.0-1ubuntu1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2build2) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.5-1) ... Setting up python3.12-dev (3.12.3-1) ... Setting up cython3 (3.0.10+dfsg-5ubuntu1) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-lxml:s390x (5.2.1-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up libxss1:s390x (1:1.2.3-1build3) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-argcomplete (3.3.0-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... Setting up python3-more-itertools (10.2.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-argh (0.31.2-1) ... Setting up libxft2:s390x (2.3.6-1build1) ... Setting up libpython3-dev:s390x (3.12.3-0ubuntu1) ... Setting up python3-cairo (1.26.0-1) ... Setting up python3-setuptools (68.1.2-2ubuntu1) ... Setting up python3-lz4 (4.0.2+dfsg-1build4) ... Setting up python3-pytest (8.1.2-1) ... Setting up libtk8.6:s390x (8.6.14-1build1) ... Setting up python3-all (3.12.3-0ubuntu1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up libpython3-all-dev:s390x (3.12.3-0ubuntu1) ... Setting up python3-dev (3.12.3-0ubuntu1) ... Setting up python3-numpy (1:1.26.4+ds-6ubuntu1) ... Setting up python3-reportlab (4.2.0-2) ... Setting up python3-contourpy (1.0.7-3) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.12.3-0ubuntu1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... Setting up python3-scipy (1.11.4-6build1) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up blt (2.5.3+dfsg-7build1) ... Setting up python3-tk:s390x (3.12.3-0ubuntu1) ... Setting up python3-pil.imagetk:s390x (10.2.0-1ubuntu1) ... Setting up python3-pyfaidx (0.8.1.1-2) ... Setting up python3-fonttools (4.46.0-1build2) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1ubuntu5) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... Processing triggers for systemd (256~rc1-1~exp2ubuntu1) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-2) ... Setting up python3-gffutils (0.13-1) ... Setting up bcftools (1.20-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:46:06 UTC 2024 s390x (s390x) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu10 g++-13_13.2.0-24ubuntu1 gcc-13_13.2.0-24ubuntu1 libc6-dev_2.39-0ubuntu8.1 libstdc++-13-dev_13.2.0-24ubuntu1 libstdc++6_14-20240429-1ubuntu1 linux-libc-dev_6.8.0-31.31 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.9.2 apt-utils_2.9.2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13.1ubuntu1 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.13.0-1 bcftools_1.20-1 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-s390x-linux-gnu_2.42-4ubuntu2 blt_2.5.3+dfsg-7build1 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-24ubuntu1 cpp-13-s390x-linux-gnu_13.2.0-24ubuntu1 cpp-s390x-linux-gnu_4:13.2.0-7ubuntu1 cython3_3.0.10+dfsg-5ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86ubuntu1 debconf-i18n_1.5.86ubuntu1 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 dh-autoreconf_20 dh-python_6.20240422 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 dpkg_1.22.6ubuntu10 dpkg-dev_1.22.6ubuntu10 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.34-1 file_1:5.45-3build1 findutils_4.9.0-5build1 fontconfig-config_2.15.0-1.1ubuntu2 fonts-dejavu-core_2.37-8 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libaudit1_1:3.1.2-2.1build1 libbinutils_2.42-4ubuntu2 libblas3_3.12.0-3build1 libblkid1_2.39.3-9ubuntu6 libbrotli1_1.1.0-2build2 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-0ubuntu8.1 libc-dev-bin_2.39-0ubuntu8.1 libc6_2.39-0ubuntu8.1 libc6-dev_2.39-0ubuntu8.1 libcairo2_1.18.0-3build1 libcap-ng0_0.8.5-1 libcap2_1:2.66-5ubuntu2 libcc1-0_14-20240429-1ubuntu1 libcom-err2_1.47.0-2.4~exp1ubuntu4 libcrypt-dev_1:4.4.36-4build1 libcrypt1_1:4.4.36-4build1 libcryptsetup12_2:2.7.0-1ubuntu4 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libcurl3t64-gnutls_8.5.0-2ubuntu10.1 libcurl4-gnutls-dev_8.5.0-2ubuntu10.1 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdeflate-dev_1.20-1 libdeflate0_1.20-1 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdpkg-perl_1.22.6ubuntu10 libdw1t64_0.191-1 libelf1t64_0.191-1 libexpat1_2.6.2-1 libexpat1-dev_2.6.2-1 libext2fs2t64_1.47.0-2.4~exp1ubuntu4 libfakeroot_1.34-1 libfdisk1_2.39.3-9ubuntu6 libffi8_3.4.6-1build1 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python3-all_3.12.3-0ubuntu1 python3-all-dev_3.12.3-0ubuntu1 python3-appdirs_1.4.4-4 python3-argcomplete_3.3.0-1 python3-argh_0.31.2-1 python3-attr_23.2.0-2 python3-biopython_1.83+dfsg1-2 python3-brotli_1.1.0-2build2 python3-cairo_1.26.0-1 python3-chardet_5.2.0+dfsg-1 python3-contourpy_1.0.7-3 python3-cycler_0.12.1-1 python3-dateutil_2.9.0-2 python3-decorator_5.1.1-5 python3-dev_3.12.3-0ubuntu1 python3-fonttools_4.46.0-1build2 python3-freetype_2.4.0-1 python3-fs_2.4.16-4 python3-gffutils_0.13-1 python3-importlib-metadata_4.12.0-1 python3-iniconfig_1.1.1-2 python3-kiwisolver_1.4.5-1 python3-lxml_5.2.1-1 python3-lz4_4.0.2+dfsg-1build4 python3-matplotlib_3.6.3-1ubuntu5 python3-minimal_3.12.3-0ubuntu1 python3-more-itertools_10.2.0-1 python3-mpmath_1.3.0-1 python3-numpy_1:1.26.4+ds-6ubuntu1 python3-packaging_24.0-1 python3-pil_10.2.0-1ubuntu1 python3-pil.imagetk_10.2.0-1ubuntu1 python3-pkg-resources_68.1.2-2ubuntu1 python3-pluggy_1.5.0-1 python3-pyfaidx_0.8.1.1-2 python3-pyparsing_3.1.2-1 python3-pytest_8.1.2-1 python3-reportlab_4.2.0-2 python3-rlpycairo_0.3.0-3 python3-scipy_1.11.4-6build1 python3-setuptools_68.1.2-2ubuntu1 python3-simplejson_3.19.2-1build2 python3-six_1.16.0-6 python3-sympy_1.12-7 python3-tk_3.12.3-0ubuntu1 python3-tz_2024.1-2 python3-ufolib2_0.16.0+dfsg1-1 python3-zipp_1.0.0-6 python3.12_3.12.3-1 python3.12-dev_3.12.3-1 python3.12-minimal_3.12.3-1 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu7 samtools_1.19.2-1build2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2build1 sensible-utils_0.0.22 sgml-base_1.31 systemd_256~rc1-1~exp2ubuntu1 systemd-dev_256~rc1-1~exp2ubuntu1 systemd-sysv_256~rc1-1~exp2ubuntu1 sysvinit-utils_3.08-6ubuntu3 tabix_1.19+ds-1.1build3 tar_1.35+dfsg-3build1 tk8.6-blt2.5_2.5.3+dfsg-7build1 tzdata_2024a-4ubuntu1 ubuntu-keyring_2023.11.28.1 unicode-data_15.1.0-1 util-linux_2.39.3-9ubuntu6 uuid-runtime_2.39.3-9ubuntu6 w3c-sgml-lib_1.3-3 x11-common_1:7.7+23ubuntu3 xfonts-encodings_1:1.0.5-0ubuntu2 xfonts-utils_1:7.7+6build3 xml-core_0.19 xz-utils_5.6.1+really5.4.5-1 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: python-pysam Binary: python3-pysam, python-pysam-tests Architecture: any all Version: 0.22.1+ds-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://pysam.readthedocs.org/en/latest Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/python-pysam Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git Testsuite: autopkgtest, autopkgtest-pkg-python Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 13), dh-sequence-python3, libhts-dev (>= 1.14~), zlib1g-dev, python3-all-dev, python3-setuptools, cython3, tabix , samtools , bcftools , python3-pytest Package-List: python-pysam-tests deb python optional arch=all python3-pysam deb python optional arch=any Checksums-Sha1: 91eb34a3a492be5e49a85dc778e42c6575db747d 1446556 python-pysam_0.22.1+ds.orig.tar.xz 47281db4e6ba2a4596cab0eceeb66f63e7913f40 10220 python-pysam_0.22.1+ds-1.debian.tar.xz Checksums-Sha256: 914b84cc5af647c783433c27513a6829e516df436fd1377adfd1a52607fafabb 1446556 python-pysam_0.22.1+ds.orig.tar.xz 3f130e2da3c479614af99d54214439dab78c198fa8f85bf127faa1abfa491b26 10220 python-pysam_0.22.1+ds-1.debian.tar.xz Files: 386ba6bde0ffe8d0700579bc8f884227 1446556 python-pysam_0.22.1+ds.orig.tar.xz a7554862a6cb87e0f458a81ae179ca2c 10220 python-pysam_0.22.1+ds-1.debian.tar.xz Dgit: 1f7b1473a937cbf7213894136dda897f0532357c debian archive/debian/0.22.1+ds-1 https://git.dgit.debian.org/python-pysam -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmZBAtsUHGVtb2xsaWVy 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signature for ./python-pysam_0.22.1+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting python-pysam in /<> dpkg-source: info: unpacking python-pysam_0.22.1+ds.orig.tar.xz dpkg-source: info: unpacking python-pysam_0.22.1+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_remote.patch dpkg-source: info: applying clean_less dpkg-source: info: applying skip-test-on-32-bit.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-28441281 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28441281 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28441281 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 python-pysam dpkg-buildpackage: info: source version 0.22.1+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/<>/tests/pysam_data' rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz make[1]: Leaving directory '/<>/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/tests/cbcf_data' rm -f all.stamp *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean I: pybuild base:311: python3.12 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/<>/.pybuild/cpython3_3.12_pysam/build' (and everything under it) 'build/bdist.linux-s390x' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:311: python3.12 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/__init__.py -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/utils.py -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/bcftools.py -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/Pileup.py -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/version.py -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/samtools.py -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/config.py -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam creating /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'pysam/libc*.c' warning: no files found matching 'win32/*.[ch]' warning: no files found matching 'htslib/LICENSE' warning: no files found matching 'htslib/README' warning: no files found matching '*.[ch]' under directory 'htslib' warning: no previously-included files found matching 'htslib/*config*.h' warning: no files found matching 'htslib/configure.ac' warning: no files found matching 'htslib/m4/*.m4' warning: no files found matching 'htslib/*.in' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/version.sh' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/*.mk' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/cbcftools_util.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/htslib_util.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/htslib_util.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignedsegment.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignedsegment.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignmentfile.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcalignmentfile.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcf.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcf.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcf.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcftools.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbcftools.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbgzf.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcbgzf.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcfaidx.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcfaidx.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libchtslib.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libchtslib.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libchtslib.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamfile.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamfile.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamtools.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamtools.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcsamtools.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabix.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabix.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabixproxies.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libctabixproxies.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcutils.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcutils.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcvcf.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/libcvcf.pyx -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/py.typed -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/pysam_util.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/pysam_util.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/version.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam copying pysam/version.pyi -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam creating /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/LICENSE -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/README -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/amplicon_stats.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam2depth.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_addrprg.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_aux.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_cat.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_color.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_consensus.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_fastq.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_flags.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_import.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_index.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_markdup.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_mate.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_md.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_plcmd.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_quickcheck.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_reheader.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_rmdup.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_rmdupse.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_samples.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_sort.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_split.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_stat.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bamshuf.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bamtk.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bedcov.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bedidx.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/coverage.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/coverage.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/cram_size.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/cut_target.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/dict.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/dict.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/faidx.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/faidx.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/padding.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/padding.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/phase.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/phase.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/reference.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/reference.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/reset.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/reset.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_opts.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_utils.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_utils.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_view.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sample.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sample.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/splaysort.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/stats.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/stats.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/stats_isize.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/tmp_file.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools copying samtools/version.sh -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools creating /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools/lz4 copying samtools/config.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/samtools creating /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/HMM.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/LICENSE -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/README -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/abuf.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/abuf.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bin.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/ccall.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/cigar_state.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/cols.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/cols.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/consensus.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/convert.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/csq.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/dbuf.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/dist.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/dist.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/em.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/em.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/extsort.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/extsort.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/filter.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gff.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gff.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gvcf.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/hclust.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/hex.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/kmin.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/main.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/main.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/mcall.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/mpileup.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/ploidy.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/prob1.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/read_consensus.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/read_consensus.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/regidx.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/reheader.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/str_finder.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/str_finder.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/tabix.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/utlist.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/variantkey.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfannotate.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfcall.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfcnv.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfconcat.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfconvert.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcffilter.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfhead.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfindex.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfisec.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfmerge.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfnorm.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfplugin.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfquery.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfroh.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfsom.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfsort.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfstats.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfview.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcmp.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/version.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/version.c.pysam.c -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/version.sh -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/.pybuild/cpython3_3.12_pysam/build/pysam/include/bcftools running build_ext Compiling pysam/libchtslib.pyx because it changed. [1/1] Cythonizing pysam/libchtslib.pyx building 'pysam.libchtslib' extension creating build creating build/temp.linux-s390x-cpython-312 creating build/temp.linux-s390x-cpython-312/pysam s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/htslib_util.c -o build/temp.linux-s390x-cpython-312/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libchtslib.c -o build/temp.linux-s390x-cpython-312/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/htslib_util.o build/temp.linux-s390x-cpython-312/pysam/libchtslib.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libchtslib.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension Compiling pysam/libcsamtools.pyx because it changed. [1/1] Cythonizing pysam/libcsamtools.pyx building 'pysam.libcsamtools' extension creating build/temp.linux-s390x-cpython-312/samtools creating build/temp.linux-s390x-cpython-312/samtools/lz4 s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libcsamtools.c -o build/temp.linux-s390x-cpython-312/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_color.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_import.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_index.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_md.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra’: samtools/bam_sort.c.pysam.c:2986:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2986 | seq[j] = comp[tmp]; | ~~~~~~~^~~~~~~~~~~ samtools/bam_sort.c.pysam.c:2973:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2973 | char seq_[10000], *seq = seq_; | ^~~~ s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_split.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bamtk.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bedcov.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/bedidx.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/coverage.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/cram_size.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/cut_target.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/dict.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/faidx.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/lz4/lz4.c -o build/temp.linux-s390x-cpython-312/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/padding.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/phase.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/reference.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/reset.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/sam_view.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/sample.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/samtools.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/stats.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-s390x-cpython-312/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/libcsamtools.o build/temp.linux-s390x-cpython-312/samtools/amplicon_stats.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam2depth.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_addrprg.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_aux.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_cat.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_color.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_consensus.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_fastq.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_flags.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_import.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_index.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_lpileup.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_markdup.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_mate.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_md.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_plbuf.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_plcmd.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_quickcheck.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_reheader.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_rmdup.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_rmdupse.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_samples.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_sort.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_split.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bam_stat.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bamshuf.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bamtk.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bedcov.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/bedidx.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/consensus_pileup.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/coverage.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/cram_size.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/cut_target.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/dict.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/faidx.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/lz4/lz4.o build/temp.linux-s390x-cpython-312/samtools/padding.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/phase.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/reference.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/reset.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/sam_opts.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/sam_utils.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/sam_view.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/sample.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/samtools.pysam.o build/temp.linux-s390x-cpython-312/samtools/stats.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/stats_isize.c.pysam.o build/temp.linux-s390x-cpython-312/samtools/tmp_file.c.pysam.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamtools.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcftools.pyx because it changed. [1/1] Cythonizing pysam/libcbcftools.pyx building 'pysam.libcbcftools' extension creating build/temp.linux-s390x-cpython-312/bcftools s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/HMM.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/abuf.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/bcftools.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/bin.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/ccall.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/cols.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/consensus.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/convert.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/csq.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/dist.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/em.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/extsort.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/filter.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/gff.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/gff.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/hclust.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/kmin.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/main.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/mcall.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/prob1.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/regidx.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/reheader.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/tabix.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:860:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 860 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:30, from /usr/include/htslib/hts.h:37, from /usr/include/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c bcftools/version.c.pysam.c -o build/temp.linux-s390x-cpython-312/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libcbcftools.c -o build/temp.linux-s390x-cpython-312/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/bcftools/HMM.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/abuf.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bam_sample.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bcftools.pysam.o build/temp.linux-s390x-cpython-312/bcftools/bin.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/ccall.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/cols.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/consensus.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/convert.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/csq.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/dist.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/em.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/extsort.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/filter.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/gff.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/gvcf.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/hclust.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/kmin.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/main.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/mcall.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/mpileup.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/ploidy.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/prob1.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/read_consensus.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/regidx.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/reheader.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/smpl_ilist.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/str_finder.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/tabix.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/tsv2vcf.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfannotate.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfbuf.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfcall.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfcnv.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfconcat.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfconvert.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcffilter.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfhead.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfindex.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfisec.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfmerge.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfnorm.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfplugin.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfquery.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfroh.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfsom.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfsort.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfstats.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcfview.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/vcmp.c.pysam.o build/temp.linux-s390x-cpython-312/bcftools/version.c.pysam.o build/temp.linux-s390x-cpython-312/pysam/libcbcftools.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcftools.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcutils.pyx because it changed. [1/1] Cythonizing pysam/libcutils.pyx building 'pysam.libcutils' extension s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libcutils.c -o build/temp.linux-s390x-cpython-312/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/pysam_util.c -o build/temp.linux-s390x-cpython-312/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/libcutils.o build/temp.linux-s390x-cpython-312/pysam/pysam_util.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -lcsamtools.cpython-312-s390x-linux-gnu -lcbcftools.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libcutils.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignmentfile.pyx:2567:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2572:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2577:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2616:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2621:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2626:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation Compiling pysam/libcalignmentfile.pyx because it changed. [1/1] Cythonizing pysam/libcalignmentfile.pyx building 'pysam.libcalignmentfile' extension s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libcalignmentfile.c -o build/temp.linux-s390x-cpython-312/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:20526:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20526 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:37152:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37152 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/libcalignmentfile.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignmentfile.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcsamfile.pyx because it changed. [1/1] Cythonizing pysam/libcsamfile.pyx building 'pysam.libcsamfile' extension s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libcsamfile.c -o build/temp.linux-s390x-cpython-312/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/libcsamfile.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libcsamfile.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignedsegment.pyx:760:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: pysam/libcalignedsegment.pyx:760:32: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. Compiling pysam/libcalignedsegment.pyx because it changed. [1/1] Cythonizing pysam/libcalignedsegment.pyx building 'pysam.libcalignedsegment' extension s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libcalignedsegment.c -o build/temp.linux-s390x-cpython-312/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/libcalignedsegment.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libcalignedsegment.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabix.pyx because it changed. [1/1] Cythonizing pysam/libctabix.pyx building 'pysam.libctabix' extension s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libctabix.c -o build/temp.linux-s390x-cpython-312/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/libctabix.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libctabix.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcfaidx.pyx because it changed. [1/1] Cythonizing pysam/libcfaidx.pyx building 'pysam.libcfaidx' extension s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libcfaidx.c -o build/temp.linux-s390x-cpython-312/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/libcfaidx.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libcfaidx.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcf.pyx because it changed. [1/1] Cythonizing pysam/libcbcf.pyx building 'pysam.libcbcf' extension s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libcbcf.c -o build/temp.linux-s390x-cpython-312/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: pysam/libcbcf.c:85908:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85908 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: pysam/libcbcf.c:80586:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80586 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’: pysam/libcbcf.c:44304:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44304 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:44330:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44330 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’: pysam/libcbcf.c:80281:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80281 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/libcbcf.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libcbcf.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbgzf.pyx because it changed. [1/1] Cythonizing pysam/libcbgzf.pyx building 'pysam.libcbgzf' extension s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libcbgzf.c -o build/temp.linux-s390x-cpython-312/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/libcbgzf.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libcbgzf.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabixproxies.pyx because it changed. [1/1] Cythonizing pysam/libctabixproxies.pyx building 'pysam.libctabixproxies' extension s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libctabixproxies.c -o build/temp.linux-s390x-cpython-312/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/libctabixproxies.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libctabixproxies.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcvcf.pyx:1083:27: Unreachable code Compiling pysam/libcvcf.pyx because it changed. [1/1] Cythonizing pysam/libcvcf.pyx building 'pysam.libcvcf' extension s390x-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.12 -c pysam/libcvcf.c -o build/temp.linux-s390x-cpython-312/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra’: pysam/libcvcf.c:30033:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 30033 | __pyx_t_11 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:24986:10: note: ‘__pyx_v_qual’ was declared here 24986 | double __pyx_v_qual; | ^~~~~~~~~~~~ s390x-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -mbackchain -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.22.1+ds-1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-s390x-cpython-312/pysam/libcvcf.o -L/<>/pysam -L/usr/lib/s390x-linux-gnu -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/<>/.pybuild/cpython3_3.12_pysam/build/pysam -L/usr/lib/s390x-linux-gnu -lz -lhts -lchtslib.cpython-312-s390x-linux-gnu -lcutils.cpython-312-s390x-linux-gnu -o /<>/.pybuild/cpython3_3.12_pysam/build/pysam/libcvcf.cpython-312-s390x-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Entering directory '/<>' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/<>/tests/pysam_data' samtools faidx ex1.fa samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz [mpileup] 1 samples in 1 input files gunzip < ex1.sam.gz > ex1.sam samtools index ex1.bam samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view --no-PG -bo ex2.bam ex2.sam samtools index ex2.bam samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 gunzip < with_md.sam.gz > with_md.sam samtools view --no-PG -bo with_md.bam with_md.sam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated samtools index with_md.bam samtools view --no-PG -bu -o uncompressed.bam ex2.sam samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam samtools view --no-PG -bo MM-double.bam MM-double.sam samtools view --no-PG -bo MM-multi.bam MM-multi.sam samtools view --no-PG -bo MM-orient.bam MM-orient.sam samtools view --no-PG -bo ex10.bam ex10.sam samtools view --no-PG -bo ex3.bam ex3.sam samtools view --no-PG -bo ex4.bam ex4.sam samtools view --no-PG -bo ex5.bam ex5.sam samtools view --no-PG -bo ex6.bam ex6.sam samtools view --no-PG -bo ex8.bam ex8.sam samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam samtools view --no-PG -bo example_btag.bam example_btag.sam samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam touch tmp.list samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam rm -f tmp.list samtools view --no-PG -bo issue100.bam issue100.sam samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam samtools view --no-PG -bo softclip.bam softclip.sam samtools view --no-PG -bo tag_bug.bam tag_bug.sam samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam samtools view --no-PG -bo test_query_position.bam test_query_position.sam samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam samtools index MM-chebi.bam samtools index MM-double.bam samtools index MM-multi.bam samtools index MM-orient.bam samtools index ex10.bam samtools index ex3.bam samtools index ex4.bam samtools index ex5.bam samtools index ex6.bam samtools index ex8.bam samtools index ex9_fail.bam samtools index ex9_nofail.bam samtools index ex_spliced.bam samtools index example_aligned_pairs.bam samtools index example_btag.bam samtools index example_dash_in_chr.bam samtools index example_empty_header.bam samtools index example_empty_with_header.bam samtools index example_reverse_complement.bam samtools index example_unmapped_reads_no_sq.bam samtools index issue100.bam samtools index rg_with_tab.bam samtools index softclip.bam samtools index tag_bug.bam samtools index test_mapped_unmapped.bam samtools index test_query_position.bam samtools index test_unaligned.bam samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam samtools index ex1.cram samtools index ex2.cram samtools index ex3.cram cp ex1.bam example_bai.bam samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 1+0 records in 1+0 records out 122288 bytes (122 kB, 119 KiB) copied, 0.000264751 s, 462 MB/s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - samtools index empty.bam cp ex1.bam explicit_index.bam cp ex1.cram explicit_index.cram gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz bgzip < ex1.fa > ex1.fa.gz samtools faidx ex1.fa.gz cp ex1.bam ex1_csi.bam samtools index -c ex1_csi.bam touch all.stamp rm with_md.sam make[2]: Leaving directory '/<>/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/<>/tests/cbcf_data' bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index bgzip < example_vcf42.vcf > example_vcf42.vcf.gz tabix -p vcf example_vcf42.vcf.gz # create tbi index bcftools index example_vcf42.vcf.gz # create csi index bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index bcftools index example_vcf42_only_header.vcf.gz # create csi index bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index bcftools index example_vcf42_withcontigs.vcf.gz # create csi index bgzip < example_vcf43.vcf > example_vcf43.vcf.gz tabix -p vcf example_vcf43.vcf.gz # create tbi index bcftools index example_vcf43.vcf.gz # create csi index bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index bcftools index example_vcf43_with_utf8.vcf.gz # create csi index bgzip < gnomad.vcf > gnomad.vcf.gz tabix -p vcf gnomad.vcf.gz # create tbi index bcftools index gnomad.vcf.gz # create csi index bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz tabix -p vcf gnomad_fixed.vcf.gz # create tbi index bcftools index gnomad_fixed.vcf.gz # create csi index bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz tabix -p vcf missing_genotypes.vcf.gz # create tbi index bcftools index missing_genotypes.vcf.gz # create csi index bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf bcftools index example_vcf40.bcf bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf bcftools index example_vcf42.bcf bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf bcftools index example_vcf42_only_header.bcf bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf bcftools index example_vcf42_withcontigs.bcf bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf bcftools index example_vcf43.bcf bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf bcftools index example_vcf43_with_utf8.bcf bcftools view -O b gnomad.vcf.gz -o gnomad.bcf bcftools index gnomad.bcf bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools index gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf touch all.stamp make[2]: Leaving directory '/<>/tests/cbcf_data' dh_auto_test I: pybuild base:311: cd /<>/.pybuild/cpython3_3.12_pysam/build; python3.12 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.12.3, pytest-8.1.2, pluggy-1.5.0 -- /usr/bin/python3.12 cachedir: .pytest_cache rootdir: /<> configfile: setup.cfg collecting ... collected 951 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_1character_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_bad_type_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags Fatal Python error: Segmentation fault Current thread 0x000003ff894fb0c0 (most recent call first): File "/<>/.pybuild/cpython3_3.12_pysam/build/tests/AlignedSegment_test.py", line 1439 in c File "/<>/.pybuild/cpython3_3.12_pysam/build/tests/AlignedSegment_test.py", line 1442 in testArrayTags File "/usr/lib/python3.12/unittest/case.py", line 589 in _callTestMethod File "/usr/lib/python3.12/unittest/case.py", line 634 in run File "/usr/lib/python3.12/unittest/case.py", line 690 in __call__ File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 321 in runtest File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 172 in pytest_runtest_call File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 240 in File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 340 in from_call File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 239 in call_and_report File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 134 in runtestprotocol File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 115 in pytest_runtest_protocol File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/main.py", line 364 in pytest_runtestloop File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/main.py", line 339 in _main File "/usr/lib/python3/dist-packages/_pytest/main.py", line 285 in wrap_session File "/usr/lib/python3/dist-packages/_pytest/main.py", line 332 in pytest_cmdline_main File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 103 in _multicall File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513 in __call__ File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 174 in main File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 197 in console_main File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 7 in File "", line 88 in _run_code File "", line 198 in _run_module_as_main Extension modules: pysam.libcutils, pysam.libchtslib, pysam.libcsamtools, pysam.libcbcftools, pysam.libcfaidx, pysam.libctabixproxies, pysam.libctabix, pysam.libcalignmentfile, pysam.libcalignedsegment, pysam.libcsamfile, pysam.libcvcf, pysam.libcbcf, pysam.libcbgzf (total: 13) Segmentation fault (core dumped) E: pybuild pybuild:389: test: plugin distutils failed with: exit code=139: cd /<>/.pybuild/cpython3_3.12_pysam/build; python3.12 -m pytest tests dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.12 returned exit code 13 make[1]: *** [debian/rules:31: override_dh_auto_test] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:22: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2024-05-12T23:35:41Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: 152564 Build-Time: 356 Distribution: oracular-proposed Fail-Stage: build Host Architecture: s390x Install-Time: 100 Job: python-pysam_0.22.1+ds-1.dsc Machine Architecture: s390x Package: python-pysam Package-Time: 457 Source-Version: 0.22.1+ds-1 Space: 152564 Status: attempted Version: 0.22.1+ds-1 -------------------------------------------------------------------------------- Finished at 2024-05-12T23:35:41Z Build needed 00:07:37, 152564k disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=oracular --arch=s390x PACKAGEBUILD-28441281 Scanning for processes to kill in build PACKAGEBUILD-28441281