https://launchpad.net/ubuntu/+source/python-pysam/0.20.0+ds-3build1/+build/25688808 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lgw01-090 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 Buildd toolchain package versions: launchpad-buildd_230~623~ubuntu20.04.1 python3-lpbuildd_230~623~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 22 Mar 05:40:42 ntpdate[180885]: adjust time server 10.211.37.1 offset -0.000848 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25688808 --image-type chroot /home/buildd/filecache-default/859743d4aa431be74cb50b11ddbd51d0d1ab094f Creating target for build PACKAGEBUILD-25688808 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25688808 Starting target for build PACKAGEBUILD-25688808 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25688808 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-25688808 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25688808 Updating target for build PACKAGEBUILD-25688808 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main riscv64 Packages [1314 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe riscv64 Packages [13.9 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5932 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 Packages [63.2 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [35.5 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe riscv64 Packages [108 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [53.0 kB] Fetched 22.4 MB in 30s (737 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-13-base libproc2-0 The following packages will be upgraded: adduser advancecomp apt bash binutils binutils-common binutils-riscv64-linux-gnu ca-certificates coreutils cpp cpp-12 dash debconf diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-12 gcc gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep hostname libacl1 libapparmor1 libapt-pkg6.0 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libext2fs2 libfakeroot libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libkmod2 liblzma5 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpcre2-8-0 libperl5.36 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libudev1 libzstd1 linux-libc-dev logsave lsb-base lto-disabled-list ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tzdata xz-utils zlib1g 105 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 88.4 MB of archives. After this operation, 894 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu lunar/main riscv64 bash riscv64 5.2.15-2ubuntu1 [672 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main riscv64 coreutils riscv64 9.1-1ubuntu2 [1309 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcrypt-dev riscv64 1:4.4.33-2 [234 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libc6-dev riscv64 2.37-0ubuntu2 [3134 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libc-dev-bin riscv64 2.37-0ubuntu2 [18.8 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcrypt1 riscv64 1:4.4.33-2 [93.4 kB] Get:7 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 linux-libc-dev riscv64 6.2.0-18.18 [1474 kB] Get:8 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libc6 riscv64 2.37-0ubuntu2 [2609 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libc-bin riscv64 2.37-0ubuntu2 [551 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main riscv64 gcc-13-base riscv64 13-20230305-1ubuntu1 [40.6 kB] Get:11 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgcc-s1 riscv64 13-20230305-1ubuntu1 [57.0 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main riscv64 liblzma5 riscv64 5.4.1-0.2 [115 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgcrypt20 riscv64 1.10.1-3ubuntu1 [503 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main riscv64 libstdc++6 riscv64 13-20230305-1ubuntu1 [783 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main riscv64 libacl1 riscv64 2.3.1-3 [15.7 kB] Get:16 http://ftpmaster.internal/ubuntu lunar/main riscv64 libapparmor1 riscv64 3.0.8-1ubuntu2 [43.1 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main riscv64 libaudit-common all 1:3.0.9-1 [5142 B] Get:18 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcap-ng0 riscv64 0.8.3-1build2 [13.6 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main riscv64 libaudit1 riscv64 1:3.0.9-1 [44.0 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcap2 riscv64 1:2.66-3ubuntu2 [25.3 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main riscv64 libperl5.36 riscv64 5.36.0-7 [4197 kB] Get:22 http://ftpmaster.internal/ubuntu lunar/main riscv64 perl riscv64 5.36.0-7 [235 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main riscv64 perl-base riscv64 5.36.0-7 [1649 kB] Get:24 http://ftpmaster.internal/ubuntu lunar/main riscv64 perl-modules-5.36 all 5.36.0-7 [2984 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdb5.3 riscv64 5.3.28+dfsg2-1 [691 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main riscv64 zlib1g riscv64 1:1.2.13.dfsg-1ubuntu4 [54.0 kB] Get:27 http://ftpmaster.internal/ubuntu lunar/main riscv64 debconf all 1.5.82 [125 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main riscv64 libssl3 riscv64 3.0.8-1ubuntu1 [1447 kB] Get:29 http://ftpmaster.internal/ubuntu lunar/main riscv64 libzstd1 riscv64 1.5.4+dfsg2-4 [310 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main riscv64 libkmod2 riscv64 30+20221128-1ubuntu1 [43.5 kB] Get:31 http://ftpmaster.internal/ubuntu lunar/main riscv64 libseccomp2 riscv64 2.5.4-1ubuntu3 [47.0 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main riscv64 libpcre2-8-0 riscv64 10.42-1 [142 kB] Get:33 http://ftpmaster.internal/ubuntu lunar/main riscv64 libselinux1 riscv64 3.4-1build4 [71.6 kB] Get:34 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 systemd-sysv riscv64 252.5-2ubuntu3 [11.5 kB] Get:35 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 systemd riscv64 252.5-2ubuntu3 [2815 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libsystemd-shared riscv64 252.5-2ubuntu3 [1629 kB] Get:37 http://ftpmaster.internal/ubuntu lunar/main riscv64 libatomic1 riscv64 13-20230305-1ubuntu1 [9422 B] Get:38 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcryptsetup12 riscv64 2:2.6.1-1ubuntu1 [196 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main riscv64 libp11-kit0 riscv64 0.24.1-2ubuntu1 [196 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libsystemd0 riscv64 252.5-2ubuntu3 [360 kB] Get:41 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libudev1 riscv64 252.5-2ubuntu3 [143 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main riscv64 libapt-pkg6.0 riscv64 2.6.0 [935 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main riscv64 dpkg riscv64 1.21.21ubuntu1 [1352 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main riscv64 dash riscv64 0.5.12-2ubuntu1 [81.8 kB] Get:45 http://ftpmaster.internal/ubuntu lunar/main riscv64 diffutils riscv64 1:3.8-4 [167 kB] Get:46 http://ftpmaster.internal/ubuntu lunar/main riscv64 grep riscv64 3.8-5 [155 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/main riscv64 hostname riscv64 3.23+nmu1ubuntu1 [10.5 kB] Get:48 http://ftpmaster.internal/ubuntu lunar/main riscv64 ncurses-bin riscv64 6.4-2 [177 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main riscv64 sed riscv64 4.9-1 [191 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main riscv64 ncurses-base all 6.4-2 [21.3 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main riscv64 sysvinit-utils riscv64 3.06-2ubuntu1 [32.5 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main riscv64 lsb-base all 11.6 [4606 B] Get:53 http://ftpmaster.internal/ubuntu lunar/main riscv64 adduser all 3.129ubuntu1 [59.0 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main riscv64 gpgv riscv64 2.2.40-1ubuntu2 [202 kB] Get:55 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgnutls30 riscv64 3.7.8-5ubuntu1 [897 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main riscv64 apt riscv64 2.6.0 [1348 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main riscv64 logsave riscv64 1.47.0-1ubuntu1 [13.7 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main riscv64 libext2fs2 riscv64 1.47.0-1ubuntu1 [197 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main riscv64 e2fsprogs riscv64 1.47.0-1ubuntu1 [555 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main riscv64 libattr1 riscv64 1:2.5.1-4 [11.4 kB] Get:61 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdebconfclient0 riscv64 0.267ubuntu1 [7418 B] Get:62 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsemanage-common all 3.4-1build4 [9852 B] Get:63 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsemanage2 riscv64 3.4-1build4 [83.5 kB] Get:64 http://ftpmaster.internal/ubuntu lunar/main riscv64 libncurses6 riscv64 6.4-2 [93.3 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main riscv64 libncursesw6 riscv64 6.4-2 [126 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main riscv64 libtinfo6 riscv64 6.4-2 [90.6 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcom-err2 riscv64 1.47.0-1ubuntu1 [13.5 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main riscv64 libproc2-0 riscv64 2:4.0.3-1ubuntu1 [45.2 kB] Get:69 http://ftpmaster.internal/ubuntu lunar/main riscv64 libss2 riscv64 1.47.0-1ubuntu1 [15.2 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main riscv64 procps riscv64 2:4.0.3-1ubuntu1 [598 kB] Get:71 http://ftpmaster.internal/ubuntu lunar/main riscv64 sensible-utils all 0.0.17+nmu1 [19.3 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/main riscv64 openssl riscv64 3.0.8-1ubuntu1 [1142 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/main riscv64 ca-certificates all 20230311 [155 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main riscv64 readline-common all 8.2-1.3 [55.7 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main riscv64 libreadline8 riscv64 8.2-1.3 [131 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsqlite3-0 riscv64 3.40.1-1 [583 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main riscv64 tzdata all 2022g-7ubuntu2 [270 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main riscv64 xz-utils riscv64 5.4.1-0.2 [266 kB] Get:79 http://ftpmaster.internal/ubuntu lunar/main riscv64 advancecomp riscv64 2.5-1 [216 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main riscv64 libctf0 riscv64 2.40-2ubuntu3 [87.2 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/main riscv64 libctf-nobfd0 riscv64 2.40-2ubuntu3 [89.2 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/main riscv64 binutils-riscv64-linux-gnu riscv64 2.40-2ubuntu3 [818 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/main riscv64 libbinutils riscv64 2.40-2ubuntu3 [459 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main riscv64 binutils riscv64 2.40-2ubuntu3 [2980 B] Get:85 http://ftpmaster.internal/ubuntu lunar/main riscv64 binutils-common riscv64 2.40-2ubuntu3 [218 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/main riscv64 libmpfr6 riscv64 4.2.0-1 [260 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main riscv64 g++-12 riscv64 12.2.0-17ubuntu1 [9555 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main riscv64 gcc-12 riscv64 12.2.0-17ubuntu1 [16.3 MB] Get:89 http://ftpmaster.internal/ubuntu lunar/main riscv64 cpp-12 riscv64 12.2.0-17ubuntu1 [8286 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgomp1 riscv64 13-20230305-1ubuntu1 [139 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main riscv64 libasan8 riscv64 13-20230305-1ubuntu1 [2671 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/main riscv64 libstdc++-12-dev riscv64 12.2.0-17ubuntu1 [4961 kB] Get:93 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgcc-12-dev riscv64 12.2.0-17ubuntu1 [2613 kB] Get:94 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcc1-0 riscv64 13-20230305-1ubuntu1 [45.7 kB] Get:95 http://ftpmaster.internal/ubuntu lunar/main riscv64 gcc-12-base riscv64 12.2.0-17ubuntu1 [41.4 kB] Get:96 http://ftpmaster.internal/ubuntu lunar/main riscv64 g++ riscv64 4:12.2.0-3ubuntu1 [1108 B] Get:97 http://ftpmaster.internal/ubuntu lunar/main riscv64 gcc riscv64 4:12.2.0-3ubuntu1 [5178 B] Get:98 http://ftpmaster.internal/ubuntu lunar/main riscv64 cpp riscv64 4:12.2.0-3ubuntu1 [27.8 kB] Get:99 http://ftpmaster.internal/ubuntu lunar/main riscv64 dpkg-dev all 1.21.21ubuntu1 [1117 kB] Get:100 http://ftpmaster.internal/ubuntu lunar/main riscv64 libdpkg-perl all 1.21.21ubuntu1 [247 kB] Get:101 http://ftpmaster.internal/ubuntu lunar/main riscv64 lto-disabled-list all 38 [12.3 kB] Get:102 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfakeroot riscv64 1.31-1.1 [27.6 kB] Get:103 http://ftpmaster.internal/ubuntu lunar/main riscv64 fakeroot riscv64 1.31-1.1 [67.9 kB] Get:104 http://ftpmaster.internal/ubuntu lunar/main riscv64 gpg riscv64 2.2.40-1ubuntu2 [491 kB] Get:105 http://ftpmaster.internal/ubuntu lunar/main riscv64 gpgconf riscv64 2.2.40-1ubuntu2 [119 kB] Get:106 http://ftpmaster.internal/ubuntu lunar/main riscv64 gpg-agent riscv64 2.2.40-1ubuntu2 [239 kB] Get:107 http://ftpmaster.internal/ubuntu lunar/main riscv64 pkgbinarymangler all 152 [16.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 88.4 MB in 13s (6609 kB/s) (Reading database ... 13011 files and directories currently installed.) Preparing to unpack .../bash_5.2.15-2ubuntu1_riscv64.deb ... Unpacking bash (5.2.15-2ubuntu1) over (5.2-1ubuntu2) ... Setting up bash (5.2.15-2ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 13011 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1ubuntu2_riscv64.deb ... Unpacking coreutils (9.1-1ubuntu2) over (8.32-4.1ubuntu1) ... Setting up coreutils (9.1-1ubuntu2) ... (Reading database ... 13011 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.33-2_riscv64.deb ... Unpacking libcrypt-dev:riscv64 (1:4.4.33-2) over (1:4.4.33-1) ... Preparing to unpack .../libc6-dev_2.37-0ubuntu2_riscv64.deb ... Unpacking libc6-dev:riscv64 (2.37-0ubuntu2) over (2.36-0ubuntu4) ... Preparing to unpack .../libc-dev-bin_2.37-0ubuntu2_riscv64.deb ... 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Setting up libasan8:riscv64 (13-20230305-1ubuntu1) ... Setting up procps (2:4.0.3-1ubuntu1) ... Setting up libcryptsetup12:riscv64 (2:2.6.1-1ubuntu1) ... Setting up libbinutils:riscv64 (2.40-2ubuntu3) ... Setting up libc-dev-bin (2.37-0ubuntu2) ... Setting up openssl (3.0.8-1ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.2-1.3) ... Setting up libcc1-0:riscv64 (13-20230305-1ubuntu1) ... Setting up libperl5.36:riscv64 (5.36.0-7) ... Setting up libkmod2:riscv64 (30+20221128-1ubuntu1) ... Setting up libctf0:riscv64 (2.40-2ubuntu3) ... Setting up cpp-12 (12.2.0-17ubuntu1) ... Setting up pkgbinarymangler (152) ... Setting up libreadline8:riscv64 (8.2-1.3) ... Setting up binutils-riscv64-linux-gnu (2.40-2ubuntu3) ... Setting up e2fsprogs (1.47.0-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up binutils (2.40-2ubuntu3) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 22 added, 6 removed; done. Setting up perl (5.36.0-7) ... Setting up libgcc-12-dev:riscv64 (12.2.0-17ubuntu1) ... Setting up libsystemd-shared:riscv64 (252.5-2ubuntu3) ... Setting up libdpkg-perl (1.21.21ubuntu1) ... Setting up cpp (4:12.2.0-3ubuntu1) ... Setting up gpgconf (2.2.40-1ubuntu2) ... Setting up libc6-dev:riscv64 (2.37-0ubuntu2) ... Setting up gpg (2.2.40-1ubuntu2) ... Setting up gpg-agent (2.2.40-1ubuntu2) ... Setting up libstdc++-12-dev:riscv64 (12.2.0-17ubuntu1) ... Setting up systemd (252.5-2ubuntu3) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up dpkg-dev (1.21.21ubuntu1) ... Setting up gcc-12 (12.2.0-17ubuntu1) ... Setting up g++-12 (12.2.0-17ubuntu1) ... Setting up systemd-sysv (252.5-2ubuntu3) ... Setting up gcc (4:12.2.0-3ubuntu1) ... Setting up g++ (4:12.2.0-3ubuntu1) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for ca-certificates (20230311) ... 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-25688808 riscv64 lunar-proposed -c chroot:build-PACKAGEBUILD-25688808 --arch=riscv64 --dist=lunar-proposed --nolog python-pysam_0.20.0+ds-3build1.dsc Initiating build PACKAGEBUILD-25688808 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lgw01-090.buildd +==============================================================================+ | python-pysam 0.20.0+ds-3build1 (riscv64) Wed, 22 Mar 2023 05:48:55 +0000 | +==============================================================================+ Package: python-pysam Version: 0.20.0+ds-3build1 Source Version: 0.20.0+ds-3build1 Distribution: lunar-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-25688808/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-45i3lX/resolver-QWCl4b' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.20.0+ds-3build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-pysam-45i3lX/python-pysam-0.20.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-45i3lX' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-exec, dh-python, 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-exec, dh-python, 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 [455 B] Get:5 copy:/<>/apt_archive ./ Packages [530 B] Fetched 1942 B in 1s (1713 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72 libjs-jquery libjs-sphinxdoc libjs-underscore libldap2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3 python3-all python3-all-dev python3-attr python3-dev python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pytest python3-setuptools python3.11 python3.11-dev python3.11-minimal samtools tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python3-numpy python3-matplotlib texlive-latex-recommended cython-doc dh-make flit python3-build python3-tomli python3-installer gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-attr-doc subversion python-setuptools-doc python3.11-venv python3.11-doc binfmt-support cwltool Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72 libjs-jquery libjs-sphinxdoc libjs-underscore libldap2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3 python3-all python3-all-dev python3-attr python3-dev python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pytest python3-setuptools python3.11 python3.11-dev python3.11-minimal samtools sbuild-build-depends-main-dummy tabix zlib1g-dev 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 52.2 MB of archives. After this operation, 266 MB of additional disk space will be used. 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23.0-1 [32.7 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/universe riscv64 python3-pluggy all 1.0.0+repack-1 [15.1 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/universe riscv64 python3-py all 1.11.0-1 [73.2 kB] Get:83 http://ftpmaster.internal/ubuntu lunar/universe riscv64 python3-pytest all 7.2.1-2 [237 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main riscv64 python3-setuptools all 66.1.1-1 [453 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/universe riscv64 samtools riscv64 1.16.1-1 [574 kB] Get:86 http://ftpmaster.internal/ubuntu lunar/universe riscv64 tabix riscv64 1.16+ds-3 [420 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/main riscv64 dh-exec riscv64 0.27 [24.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 52.2 MB in 10s (5274 kB/s) Selecting previously unselected package libpython3.11-minimal:riscv64. (Reading database ... 12514 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_riscv64.deb ... Unpacking libpython3.11-minimal:riscv64 (3.11.2-6) ... Selecting previously unselected package libexpat1:riscv64. Preparing to unpack .../libexpat1_2.5.0-1_riscv64.deb ... Unpacking libexpat1:riscv64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_riscv64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:riscv64 (3.11.2-6) ... Setting up libexpat1:riscv64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... 12828 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.2-1_riscv64.deb ... Unpacking python3-minimal (3.11.2-1) ... Selecting previously unselected package media-types. 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Setting up automake (1:1.16.5-1.3) ... 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 python3.11 (3.11.2-6) ... Setting up libdw1:riscv64 (0.188-2.1) ... Setting up gettext (0.21-11) ... Setting up libpython3.11:riscv64 (3.11.2-6) ... Setting up libtool (2.4.7-5) ... Setting up libcurl3-gnutls:riscv64 (7.88.1-6ubuntu2) ... Setting up python3 (3.11.2-1) ... Setting up libcurl4-gnutls-dev:riscv64 (7.88.1-6ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up python3-packaging (23.0-1) ... Setting up libpython3.11-dev:riscv64 (3.11.2-6) ... Setting up cython3 (0.29.32-2ubuntu2) ... Setting up libjs-sphinxdoc (5.3.0-3) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up debugedit (1:5.0-5) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up libhts3:riscv64 (1.16+ds-3) ... Setting up libpython3-dev:riscv64 (3.11.2-1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-pytest (7.2.1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up bcftools (1.16-1) ... Setting up libhts-dev:riscv64 (1.16+ds-3) ... Setting up python3-all (3.11.2-1) ... Setting up man-db (2.11.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up samtools (1.16.1-1) ... Setting up libpython3-all-dev:riscv64 (3.11.2-1) ... Setting up python3-dev (3.11.2-1) ... Setting up python3-all-dev (3.11.2-1) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up dh-exec (0.27) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (252.5-2ubuntu3) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 (riscv64) Toolchain package versions: binutils_2.40-2ubuntu3 dpkg-dev_1.21.21ubuntu1 g++-12_12.2.0-17ubuntu1 gcc-12_12.2.0-17ubuntu1 libc6-dev_2.37-0ubuntu2 libstdc++-12-dev_12.2.0-17ubuntu1 libstdc++6_13-20230305-1ubuntu1 linux-libc-dev_6.2.0-18.18 Package versions: adduser_3.129ubuntu1 advancecomp_2.5-1 apt_2.6.0 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-11 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 bcftools_1.16-1 binutils_2.40-2ubuntu3 binutils-common_2.40-2ubuntu3 binutils-riscv64-linux-gnu_2.40-2ubuntu3 bsdextrautils_2.38.1-4ubuntu1 bsdutils_1:2.38.1-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20230311 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-3ubuntu1 cpp-12_12.2.0-17ubuntu1 cython3_0.29.32-2ubuntu2 dash_0.5.12-2ubuntu1 debconf_1.5.82 debhelper_13.11.4ubuntu3 debianutils_5.7-0.4 debugedit_1:5.0-5 dh-autoreconf_20 dh-exec_0.27 dh-python_5.20230130 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.21.21ubuntu1 dpkg-dev_1.21.21ubuntu1 dwz_0.15-1 e2fsprogs_1.47.0-1ubuntu1 fakeroot_1.31-1.1 file_1:5.44-3 findutils_4.9.0-3ubuntu1 g++_4:12.2.0-3ubuntu1 g++-12_12.2.0-17ubuntu1 gcc_4:12.2.0-3ubuntu1 gcc-12_12.2.0-17ubuntu1 gcc-12-base_12.2.0-17ubuntu1 gcc-13-base_13-20230305-1ubuntu1 gettext_0.21-11 gettext-base_0.21-11 gpg_2.2.40-1ubuntu2 gpg-agent_2.2.40-1ubuntu2 gpgconf_2.2.40-1ubuntu2 gpgv_2.2.40-1ubuntu2 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapparmor1_3.0.8-1ubuntu2 libapt-pkg6.0_2.6.0 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_13-20230305-1ubuntu1 libassuan0_2.5.5-5 libatomic1_13-20230305-1ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40-2ubuntu3 libblkid1_2.38.1-4ubuntu1 libbrotli1_1.0.9-2build8 libbz2-1.0_1.0.8-5build1 libc-bin_2.37-0ubuntu2 libc-dev-bin_2.37-0ubuntu2 libc6_2.37-0ubuntu2 libc6-dev_2.37-0ubuntu2 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-3ubuntu2 libcc1-0_13-20230305-1ubuntu1 libcom-err2_1.47.0-1ubuntu1 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libcryptsetup12_2:2.6.1-1ubuntu1 libctf-nobfd0_2.40-2ubuntu3 libctf0_2.40-2ubuntu3 libcurl3-gnutls_7.88.1-6ubuntu2 libcurl4-gnutls-dev_7.88.1-6ubuntu2 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.267ubuntu1 libdebhelper-perl_13.11.4ubuntu3 libdeflate-dev_1.15-1 libdeflate0_1.15-1 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.21ubuntu1 libdw1_0.188-2.1 libelf1_0.188-2.1 libexpat1_2.5.0-1 libexpat1-dev_2.5.0-1 libext2fs2_1.47.0-1ubuntu1 libfakeroot_1.31-1.1 libfdisk1_2.38.1-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.2.0-17ubuntu1 libgcc-s1_13-20230305-1ubuntu1 libgcrypt20_1.10.1-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1ubuntu1 libgnutls30_3.7.8-5ubuntu1 libgomp1_13-20230305-1ubuntu1 libgpg-error0_1.46-1 libgssapi-krb5-2_1.20.1-1build1 libhogweed6_3.8.1-2 libhts-dev_1.16+ds-3 libhts3_1.16+ds-3 libhtscodecs2_1.3.0-4 libicu72_72.1-3ubuntu1 libidn2-0_2.3.3-1build1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libjansson4_2.14-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_5.3.0-3 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libjson-c5_0.16-2 libk5crypto3_1.20.1-1build1 libkeyutils1_1.6.3-2 libkmod2_30+20221128-1ubuntu1 libkrb5-3_1.20.1-1build1 libkrb5support0_1.20.1-1build1 libldap2_2.6.3+dfsg-1~exp1ubuntu2 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.4-1 liblzma-dev_5.4.1-0.2 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.0.4-2 libmount1_2.38.1-4ubuntu1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libncurses6_6.4-2 libncursesw6_6.4-2 libnettle8_3.8.1-2 libnghttp2-14_1.52.0-1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libp11-kit0_0.24.1-2ubuntu1 libpam-modules_1.5.2-5ubuntu1 libpam-modules-bin_1.5.2-5ubuntu1 libpam-runtime_1.5.2-5ubuntu1 libpam0g_1.5.2-5ubuntu1 libpcre2-8-0_10.42-1 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpng16-16_1.6.39-2 libproc2-0_2:4.0.3-1ubuntu1 libprocps8_2:3.3.17-7ubuntu1 libpsl5_0.21.2-1 libpython3-all-dev_3.11.2-1 libpython3-dev_3.11.2-1 libpython3-stdlib_3.11.2-1 libpython3.11_3.11.2-6 libpython3.11-dev_3.11.2-6 libpython3.11-minimal_3.11.2-6 libpython3.11-stdlib_3.11.2-6 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg-10 libsasl2-modules-db_2.1.28+dfsg-10 libseccomp2_2.5.4-1ubuntu3 libselinux1_3.4-1build4 libsemanage-common_3.4-1build4 libsemanage2_3.4-1build4 libsepol2_3.4-2 libsmartcols1_2.38.1-4ubuntu1 libsqlite3-0_3.40.1-1 libss2_1.47.0-1ubuntu1 libssh-4_0.10.4-2 libssl3_3.0.8-1ubuntu1 libstdc++-12-dev_12.2.0-17ubuntu1 libstdc++6_13-20230305-1ubuntu1 libsub-override-perl_0.09-4 libsystemd-shared_252.5-2ubuntu3 libsystemd0_252.5-2ubuntu3 libtasn1-6_4.19.0-2 libtinfo6_6.4-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libuchardet0_0.0.7-1build2 libudev1_252.5-2ubuntu3 libunistring2_1.0-2 libuuid1_2.38.1-4ubuntu1 libxml2_2.9.14+dfsg-1.1build2 libxxhash0_0.8.1-1 libzstd1_1.5.4+dfsg2-4 linux-libc-dev_6.2.0-18.18 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-1ubuntu1 lsb-base_11.6 lto-disabled-list_38 m4_1.4.19-3 make_4.3-4.1build1 man-db_2.11.2-1 mawk_1.3.4.20200120-3.1 media-types_10.0.0 mount_2.38.1-4ubuntu1 ncurses-base_6.4-2 ncurses-bin_6.4-2 openssl_3.0.8-1ubuntu1 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-7 pinentry-curses_1.2.1-1ubuntu1 pkgbinarymangler_152 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.3-1ubuntu1 python3_3.11.2-1 python3-all_3.11.2-1 python3-all-dev_3.11.2-1 python3-attr_22.2.0-1 python3-dev_3.11.2-1 python3-distutils_3.11.2-2 python3-iniconfig_1.1.1-2 python3-lib2to3_3.11.2-2 python3-minimal_3.11.2-1 python3-more-itertools_8.10.0-2 python3-packaging_23.0-1 python3-pkg-resources_66.1.1-1 python3-pluggy_1.0.0+repack-1 python3-py_1.11.0-1 python3-pytest_7.2.1-2 python3-setuptools_66.1.1-1 python3.11_3.11.2-6 python3.11-dev_3.11.2-6 python3.11-minimal_3.11.2-6 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 samtools_1.16.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 systemd_252.5-2ubuntu3 systemd-sysv_252.5-2ubuntu3 sysvinit-utils_3.06-2ubuntu1 tabix_1.16+ds-3 tar_1.34+dfsg-1.1 tzdata_2022g-7ubuntu2 ubuntu-keyring_2021.03.26 usrmerge_33ubuntu1 util-linux_2.38.1-4ubuntu1 util-linux-extra_2.38.1-4ubuntu1 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1ubuntu4 zlib1g-dev_1:1.2.13.dfsg-1ubuntu4 +------------------------------------------------------------------------------+ | 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: 0.20.0+ds-3build1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Étienne Mollier Homepage: https://pysam.readthedocs.org/en/latest Standards-Version: 4.6.2 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-exec, dh-python, 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: 1a82c944f5d4269a999dc825401a1b5d7c1d87fd 1410696 python-pysam_0.20.0+ds.orig.tar.xz 8d513a20d4682b84a17dc485f48a1fd30e549633 10616 python-pysam_0.20.0+ds-3build1.debian.tar.xz Checksums-Sha256: 173795398967fb1f776811965a48af6e46ecc7f53fc863ae53e8c57fe0068142 1410696 python-pysam_0.20.0+ds.orig.tar.xz b4fe165844558cdd8aa7b1823d2a7fd4a86e77a9c7165ff32bc526d1c7d5e40a 10616 python-pysam_0.20.0+ds-3build1.debian.tar.xz Files: 247ff229711954949de58a1cac767d9b 1410696 python-pysam_0.20.0+ds.orig.tar.xz 1f0d8a82a8ea351bc224a2f6c3281837 10616 python-pysam_0.20.0+ds-3build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- 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signature for ./python-pysam_0.20.0+ds-3build1.dsc: no acceptable signature found dpkg-source: info: extracting python-pysam in /<> dpkg-source: info: unpacking python-pysam_0.20.0+ds.orig.tar.xz dpkg-source: info: unpacking python-pysam_0.20.0+ds-3build1.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 dpkg-source: info: applying disable-tests-python3.11.patch dpkg-source: info: applying python3.11.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=8 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-25688808 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-25688808 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-25688808 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 0.20.0+ds-3build1 dpkg-buildpackage: info: source distribution lunar dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 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 --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean I: pybuild base:240: python3.11 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_3.11_pysam/build' (and everything under it) 'build/bdist.linux-riscv64' does not exist -- can't clean it 'build/scripts-3.11' 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 --with python3 --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:240: python3.11 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:240: /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_3.11_pysam/build/pysam copying pysam/version.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/__init__.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/Pileup.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/samtools.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/config.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/utils.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/bcftools.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam creating /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include copying pysam/libchtslib.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamtools.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcf.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/version.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/cbcftools_util.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/pysam_util.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/htslib_util.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/py.typed -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignedsegment.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcutils.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabixproxies.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libchtslib.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcvcf.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/version.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignmentfile.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamfile.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcftools.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbgzf.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcfaidx.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcf.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamtools.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabix.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam creating /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/splaysort.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/config.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sample.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools creating /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/dist.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/variantkey.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/extsort.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/utlist.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/dbuf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/str_finder.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/hex.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/abuf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/cols.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libchtslib.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcsamtools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcbcftools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcutils.pyx to pysam/libcutils.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcalignmentfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcalignmentfile.pyx:2573:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2578:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2583:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2622:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2627:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2632:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcsamfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcalignedsegment.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabix.pyx to pysam/libctabix.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libctabix.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcfaidx.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcf.pyx to pysam/libcbcf.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcbcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcbgzf.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libctabixproxies.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcvcf.pyx to pysam/libcvcf.c /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/pysam/libcvcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libchtslib' extension creating build creating build/temp.linux-riscv64-cpython-311 creating build/temp.linux-riscv64-cpython-311/pysam riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/htslib_util.c -o build/temp.linux-riscv64-cpython-311/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libchtslib.c -o build/temp.linux-riscv64-cpython-311/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/htslib_util.o build/temp.linux-riscv64-cpython-311/pysam/libchtslib.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.linux-riscv64-cpython-311/samtools creating build/temp.linux-riscv64-cpython-311/samtools/lz4 riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcsamtools.c -o build/temp.linux-riscv64-cpython-311/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_color.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_import.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_index.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_md.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_split.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bamtk.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bedcov.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/bedidx.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/coverage.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/cut_target.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/dict.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/faidx.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/lz4/lz4.c -o build/temp.linux-riscv64-cpython-311/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/padding.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/phase.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/reference.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/sam_view.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/sample.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/samtools.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/stats.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-riscv64-cpython-311/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcsamtools.o build/temp.linux-riscv64-cpython-311/samtools/amplicon_stats.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam2depth.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_addrprg.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_aux.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_cat.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_color.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_consensus.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_fastq.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_flags.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_import.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_index.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_lpileup.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_markdup.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_mate.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_md.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_plbuf.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_plcmd.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_quickcheck.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_reheader.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_rmdup.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_rmdupse.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_samples.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_sort.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_split.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_stat.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bamshuf.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bamtk.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bedcov.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bedidx.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/consensus_pileup.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/coverage.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/cut_target.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/dict.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/faidx.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/lz4/lz4.o build/temp.linux-riscv64-cpython-311/samtools/padding.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/phase.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/reference.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/sam_opts.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/sam_utils.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/sam_view.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/sample.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/samtools.pysam.o build/temp.linux-riscv64-cpython-311/samtools/stats.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/stats_isize.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/tmp_file.c.pysam.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-riscv64-cpython-311/bcftools riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/HMM.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/abuf.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/bcftools.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/bin.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/ccall.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/cols.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/consensus.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/convert.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/csq.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/dist.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/em.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/extsort.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/filter.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/hclust.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/kmin.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/main.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/mcall.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/prob1.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/regidx.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/reheader.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/tabix.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-riscv64-cpython-311/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:751:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 751 | 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:556:14: note: in a call to allocation function ‘calloc’ declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c bcftools/version.c.pysam.c -o build/temp.linux-riscv64-cpython-311/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcbcftools.c -o build/temp.linux-riscv64-cpython-311/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/bcftools/HMM.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/abuf.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/bam2bcf.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/bam_sample.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/bcftools.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/bin.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/ccall.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/cols.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/consensus.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/convert.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/csq.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/dist.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/em.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/extsort.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/filter.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/gvcf.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/hclust.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/kmin.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/main.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/mcall.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/mpileup.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/ploidy.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/prob1.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/regidx.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/reheader.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/smpl_ilist.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/str_finder.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/tabix.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/tsv2vcf.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfannotate.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfbuf.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfcall.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfcnv.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfconcat.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfconvert.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcffilter.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfhead.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfindex.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfisec.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfmerge.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfnorm.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfplugin.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfquery.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfroh.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfsom.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfsort.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfstats.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfview.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcmp.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/version.c.pysam.o build/temp.linux-riscv64-cpython-311/pysam/libcbcftools.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcutils.c -o build/temp.linux-riscv64-cpython-311/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/pysam_util.c -o build/temp.linux-riscv64-cpython-311/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcutils.o build/temp.linux-riscv64-cpython-311/pysam/pysam_util.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcsamtools.cpython-311-riscv64-linux-gnu -lcbcftools.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcalignmentfile.c -o build/temp.linux-riscv64-cpython-311/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:28511:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28511 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:14228:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14228 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcalignmentfile.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-riscv64-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcsamfile.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcalignedsegment.c -o build/temp.linux-riscv64-cpython-311/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c:14652:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14652 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcalignedsegment.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libctabix.c -o build/temp.linux-riscv64-cpython-311/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libctabix.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcfaidx.c -o build/temp.linux-riscv64-cpython-311/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcfaidx.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcbcf.c -o build/temp.linux-riscv64-cpython-311/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: pysam/libcbcf.c:68189:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 68189 | (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_4__dealloc__’: pysam/libcbcf.c:67914:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 67914 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: pysam/libcbcf.c:73032:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 73032 | (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:35496:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35496 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:35522:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35522 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcbcf.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcbgzf.c -o build/temp.linux-riscv64-cpython-311/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcbgzf.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libctabixproxies.c -o build/temp.linux-riscv64-cpython-311/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libctabixproxies.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcvcf.c -o build/temp.linux-riscv64-cpython-311/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.constprop’: pysam/libcvcf.c:25229:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 25229 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:19949:10: note: ‘__pyx_v_qual’ was declared here 19949 | double __pyx_v_qual; | ^~~~~~~~~~~~ riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.20.0+ds-3build1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcvcf.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /<>/debian/python3-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py copying pysam/config.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying samtools/samtools_config_vars.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension running install_lib creating /<>/debian/python3-pysam creating /<>/debian/python3-pysam/usr creating /<>/debian/python3-pysam/usr/lib creating /<>/debian/python3-pysam/usr/lib/python3.11 creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/version.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/__init__.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/Pileup.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/py.typed -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_stream.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/samtools.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/config.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/utils.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/version.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/version.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/cbcftools_util.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_util.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/csamtools_util.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/htslib_util.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/__init__.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/consensus_pileup.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bedidx.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_plbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/splaysort.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools_config_vars.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sam_opts.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/tmp_file.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/config.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_lpileup.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/stats_isize.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools.pysam.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_ampliconclip.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sample.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/dist.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/call.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bin.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/variantkey.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/convert.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/filter.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/kheap.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/extsort.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/kmin.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/gvcf.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam2bcf.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/utlist.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/dbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/str_finder.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bcftools.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/prob1.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcmp.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/config.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/ploidy.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/rbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/regidx.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/hclust.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/hex.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/abuf.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/cols.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/mw.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/khash_str2str.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam_sample.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/HMM.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/bcftools.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/version.py to version.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/Pileup.py to Pileup.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/samtools.py to samtools.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/config.py to config.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/utils.py to utils.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/bcftools.py to bcftools.cpython-311.pyc running install_egg_info 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 'win32/*.[ch]' no previously-included directories found matching 'tests/' 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' Copying pysam.egg-info to /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam-0.20.0.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/<>' cd tests/pysam_data && /usr/bin/make clean make[2]: 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[2]: Leaving directory '/<>/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[2]: Entering directory '/<>/tests/cbcf_data' rm -f all.stamp *.gz *.tbi *.csi *.bcf make[2]: 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_install -Xtest.gtf.gz find debian -name log.txt -delete make[1]: Leaving directory '/<>' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dwz: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcf.cpython-311-riscv64-linux-gnu.so: DWARF compression not beneficial - old size 1204606 new size 1223061 dh_strip -a -O--buildsystem=pybuild debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcvcf.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 115716c6cf7375bea1d1e5fbeeb70ad4ed681231 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 bf457fbaaceabcf32ed73758f80c05966f2175ee debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcftools.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 0395e6e85efd1c9ebcc5238ee249ae806781465a debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcalignedsegment.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 4ee517e708dd5550f6bc11e4085f146b50205162 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcsamtools.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 10788c6540d026b09d88ab75efbb2ccd8912afdd debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 84aca558b6350c3bf70242429e5fbf76f67d377f debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libchtslib.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 6b9af043be017e5a332d1f69e961100d59cde2f3 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcalignmentfile.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 5c4ce057d9ad52b081d3b89883ca2c2f481b044d fde1f94e8eec759a781148e6da372fae79424d39 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcutils.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 e425fb19be0638f8382cde7d26d0f2826b54fc07 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbgzf.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 a87767ced6e8375d6c8c9499a5a96eeb0b79e15e debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 cc5c6676d921d369b4515388f68ca8bd07f68a98 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libctabix.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 bb8cc8290fdcf17279baeea0067b0dcf579451db dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 152 INFO: pkgstriptranslations version 152 pkgstriptranslations: processing python3-pysam (in debian/python3-pysam); do_strip: , oemstrip: pkgstriptranslations: processing python3-pysam-dbgsym (in debian/.debhelper/python3-pysam/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/python3-pysam/dbgsym-root/DEBIAN/control, package python3-pysam-dbgsym, directory debian/.debhelper/python3-pysam/dbgsym-root dpkg-deb: building package 'python3-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-pysam/python3-pysam-dbgsym_0.20.0+ds-3build1_riscv64.deb'. pkgstripfiles: processing control file: debian/python3-pysam/DEBIAN/control, package python3-pysam, directory debian/python3-pysam pkgstripfiles: Running PNG optimization (using 8 cpus) for package python3-pysam ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.20.0+ds-3build1_riscv64.deb'. Renaming python3-pysam-dbgsym_0.20.0+ds-3build1_riscv64.deb to python3-pysam-dbgsym_0.20.0+ds-3build1_riscv64.ddeb dpkg-genbuildinfo --build=any -O../python-pysam_0.20.0+ds-3build1_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../python-pysam_0.20.0+ds-3build1_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-03-22T06:41:22Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pysam_0.20.0+ds-3build1_riscv64.changes: ----------------------------------------------- Format: 1.8 Date: Wed, 22 Mar 2023 05:39:36 +0000 Source: python-pysam Binary: python3-pysam Built-For-Profiles: noudeb Architecture: riscv64 Version: 0.20.0+ds-3build1 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Graham Inggs Description: python3-pysam - interface for the SAM/BAM sequence alignment and mapping format ( Changes: python-pysam (0.20.0+ds-3build1) lunar; urgency=medium . * No-change rebuild with Python 3.11 only Checksums-Sha1: 50d5d4d22c9dcfb9f7ee64615719774eb9086569 7615 python-pysam_0.20.0+ds-3build1_riscv64.buildinfo 07e6a68c02fb8e87ca451e65e7f930a195f24a5f 6942772 python3-pysam-dbgsym_0.20.0+ds-3build1_riscv64.ddeb dfd6e015d1a1faed71264b2a7f5cf349a1b55768 1669088 python3-pysam_0.20.0+ds-3build1_riscv64.deb Checksums-Sha256: 6ef5b23e409becc0e8c85feaf3b3a66c8b93d7c744e1fa7c1070b7981c3fdda0 7615 python-pysam_0.20.0+ds-3build1_riscv64.buildinfo fb03217adcae6464518a42b93ebb28c9ffa687ea23225750613fc8ccd7d2f574 6942772 python3-pysam-dbgsym_0.20.0+ds-3build1_riscv64.ddeb 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python3-pysam-dbgsym_0.20.0+ds-3build1_riscv64.ddeb 7a87949eb4e98fb6a48954011a1c6764 1669088 python3-pysam_0.20.0+ds-3build1_riscv64.deb Checksums-Sha1: 07e6a68c02fb8e87ca451e65e7f930a195f24a5f 6942772 python3-pysam-dbgsym_0.20.0+ds-3build1_riscv64.ddeb dfd6e015d1a1faed71264b2a7f5cf349a1b55768 1669088 python3-pysam_0.20.0+ds-3build1_riscv64.deb Checksums-Sha256: fb03217adcae6464518a42b93ebb28c9ffa687ea23225750613fc8ccd7d2f574 6942772 python3-pysam-dbgsym_0.20.0+ds-3build1_riscv64.ddeb ebd912751be809d1c6fb47ef8858afa58cd986fcc72a1514d7a801fbb8f8f768 1669088 python3-pysam_0.20.0+ds-3build1_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Wed, 22 Mar 2023 06:41:16 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-11), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), bcftools (= 1.16-1), binutils (= 2.40-2ubuntu3), binutils-common (= 2.40-2ubuntu3), binutils-riscv64-linux-gnu (= 2.40-2ubuntu3), bsdextrautils (= 2.38.1-4ubuntu1), bsdutils (= 1:2.38.1-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 9.1-1ubuntu2), cpp (= 4:12.2.0-3ubuntu1), cpp-12 (= 12.2.0-17ubuntu1), cython3 (= 0.29.32-2ubuntu2), dash (= 0.5.12-2ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.4ubuntu3), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-exec (= 0.27), dh-python (= 5.20230130), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), dpkg (= 1.21.21ubuntu1), dpkg-dev (= 1.21.21ubuntu1), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-3ubuntu1), g++ (= 4:12.2.0-3ubuntu1), g++-12 (= 12.2.0-17ubuntu1), gcc (= 4:12.2.0-3ubuntu1), gcc-12 (= 12.2.0-17ubuntu1), gcc-12-base (= 12.2.0-17ubuntu1), gcc-13-base (= 13-20230305-1ubuntu1), gettext (= 0.21-11), gettext-base (= 0.21-11), grep (= 3.8-5), groff-base (= 1.22.4-10), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 13-20230305-1ubuntu1), libatomic1 (= 13-20230305-1ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.0.9-1), libaudit1 (= 1:3.0.9-1), libbinutils (= 2.40-2ubuntu3), libblkid1 (= 2.38.1-4ubuntu1), libbrotli1 (= 1.0.9-2build8), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.37-0ubuntu2), libc-dev-bin (= 2.37-0ubuntu2), libc6 (= 2.37-0ubuntu2), libc6-dev (= 2.37-0ubuntu2), libcap-ng0 (= 0.8.3-1build2), libcap2 (= 1:2.66-3ubuntu2), libcc1-0 (= 13-20230305-1ubuntu1), libcom-err2 (= 1.47.0-1ubuntu1), libcrypt-dev (= 1:4.4.33-2), libcrypt1 (= 1:4.4.33-2), libctf-nobfd0 (= 2.40-2ubuntu3), libctf0 (= 2.40-2ubuntu3), libcurl3-gnutls (= 7.88.1-6ubuntu2), libcurl4-gnutls-dev (= 7.88.1-6ubuntu2), libdb5.3 (= 5.3.28+dfsg2-1), libdebconfclient0 (= 0.267ubuntu1), libdebhelper-perl (= 13.11.4ubuntu3), libdeflate-dev (= 1.15-1), libdeflate0 (= 1.15-1), libdpkg-perl (= 1.21.21ubuntu1), libdw1 (= 0.188-2.1), libelf1 (= 0.188-2.1), libexpat1 (= 2.5.0-1), libexpat1-dev (= 2.5.0-1), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-12-dev (= 12.2.0-17ubuntu1), libgcc-s1 (= 13-20230305-1ubuntu1), libgcrypt20 (= 1.10.1-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgnutls30 (= 3.7.8-5ubuntu1), libgomp1 (= 13-20230305-1ubuntu1), libgpg-error0 (= 1.46-1), libgssapi-krb5-2 (= 1.20.1-1build1), libhogweed6 (= 3.8.1-2), libhts-dev (= 1.16+ds-3), libhts3 (= 1.16+ds-3), libhtscodecs2 (= 1.3.0-4), libicu72 (= 72.1-3ubuntu1), libidn2-0 (= 2.3.3-1build1), libisl23 (= 0.25-1), libjansson4 (= 2.14-2), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-sphinxdoc (= 5.3.0-3), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libk5crypto3 (= 1.20.1-1build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-1build1), libkrb5support0 (= 1.20.1-1build1), libldap2 (= 2.6.3+dfsg-1~exp1ubuntu2), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.1-0.2), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-4ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.0-1), libncurses6 (= 6.4-2), libncursesw6 (= 6.4-2), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.52.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libp11-kit0 (= 0.24.1-2ubuntu1), libpam-modules (= 1.5.2-5ubuntu1), libpam-modules-bin (= 1.5.2-5ubuntu1), libpam-runtime (= 1.5.2-5ubuntu1), libpam0g (= 1.5.2-5ubuntu1), libpcre2-8-0 (= 10.42-1), libperl5.36 (= 5.36.0-7), libpipeline1 (= 1.5.7-1), libpsl5 (= 0.21.2-1), libpython3-all-dev (= 3.11.2-1), libpython3-dev (= 3.11.2-1), libpython3-stdlib (= 3.11.2-1), libpython3.11 (= 3.11.2-6), libpython3.11-dev (= 3.11.2-6), libpython3.11-minimal (= 3.11.2-6), libpython3.11-stdlib (= 3.11.2-6), libreadline8 (= 8.2-1.3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg-10), libsasl2-modules-db (= 2.1.28+dfsg-10), libselinux1 (= 3.4-1build4), libsmartcols1 (= 2.38.1-4ubuntu1), libsqlite3-0 (= 3.40.1-1), libssh-4 (= 0.10.4-2), libssl3 (= 3.0.8-1ubuntu1), libstdc++-12-dev (= 12.2.0-17ubuntu1), libstdc++6 (= 13-20230305-1ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.5-2ubuntu3), libtasn1-6 (= 4.19.0-2), libtinfo6 (= 6.4-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.5-2ubuntu3), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-4ubuntu1), libxml2 (= 2.9.14+dfsg-1.1build2), libzstd1 (= 1.5.4+dfsg2-4), linux-libc-dev (= 6.2.0-18.18), login (= 1:4.13+dfsg1-1ubuntu1), lto-disabled-list (= 38), m4 (= 1.4.19-3), make (= 4.3-4.1build1), man-db (= 2.11.2-1), mawk (= 1.3.4.20200120-3.1), media-types (= 10.0.0), ncurses-base (= 6.4-2), ncurses-bin (= 6.4-2), patch (= 2.7.6-7build2), perl (= 5.36.0-7), perl-base (= 5.36.0-7), perl-modules-5.36 (= 5.36.0-7), po-debconf (= 1.0.21+nmu1), python3 (= 3.11.2-1), python3-all (= 3.11.2-1), python3-all-dev (= 3.11.2-1), python3-attr (= 22.2.0-1), python3-dev (= 3.11.2-1), python3-distutils (= 3.11.2-2), python3-iniconfig (= 1.1.1-2), python3-lib2to3 (= 3.11.2-2), python3-minimal (= 3.11.2-1), python3-more-itertools (= 8.10.0-2), python3-packaging (= 23.0-1), python3-pkg-resources (= 66.1.1-1), python3-pluggy (= 1.0.0+repack-1), python3-py (= 1.11.0-1), python3-pytest (= 7.2.1-2), python3-setuptools (= 66.1.1-1), python3.11 (= 3.11.2-6), python3.11-dev (= 3.11.2-6), python3.11-minimal (= 3.11.2-6), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.2-0ubuntu6), samtools (= 1.16.1-1), sed (= 4.9-1), sensible-utils (= 0.0.17+nmu1), sysvinit-utils (= 3.06-2ubuntu1), tabix (= 1.16+ds-3), tar (= 1.34+dfsg-1.1), usrmerge (= 33ubuntu1), util-linux (= 2.38.1-4ubuntu1), util-linux-extra (= 2.38.1-4ubuntu1), xz-utils (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-1ubuntu4), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu4) Environment: DEB_BUILD_OPTIONS="nocheck parallel=8" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1679463576" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python3-pysam_0.20.0+ds-3build1_riscv64.deb ------------------------------------------- new Debian package, version 2.0. size 1669088 bytes: control archive=3776 bytes. 780 bytes, 17 lines control 10281 bytes, 109 lines md5sums 277 bytes, 12 lines * postinst #!/bin/sh 390 bytes, 12 lines * prerm #!/bin/sh Package: python3-pysam Source: python-pysam Version: 0.20.0+ds-3build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4394 Depends: libc6 (>= 2.34), libhts3 (>= 1.16), zlib1g (>= 1:1.1.4), python3 (<< 3.12), python3 (>= 3.11~), python3:any Section: python Priority: optional Homepage: https://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3) Pysam is a Python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. . This package installs the module for Python 3. drwxr-xr-x root/root 0 2023-03-22 05:39 ./ drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/ drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/lib/ drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/lib/python3/ drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam-0.20.0.egg-info/ -rw-r--r-- root/root 1392 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam-0.20.0.egg-info/PKG-INFO -rw-r--r-- root/root 1 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam-0.20.0.egg-info/dependency_links.txt -rw-r--r-- root/root 1 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam-0.20.0.egg-info/not-zip-safe -rw-r--r-- root/root 6 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam-0.20.0.egg-info/top_level.txt drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam/ -rw-r--r-- root/root 8955 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/Pileup.py -rw-r--r-- root/root 3491 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam/__init__.py -rw-r--r-- root/root 499 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/bcftools.py -rw-r--r-- root/root 102 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/cbcftools_util.h -rw-r--r-- root/root 16 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam/config.py -rw-r--r-- root/root 102 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/csamtools_util.h -rw-r--r-- root/root 2565 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/htslib_util.h drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam/include/ -rw-r--r-- root/root 0 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/__init__.py drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam/include/bcftools/ -rw-r--r-- root/root 5022 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/HMM.h -rw-r--r-- root/root 2521 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/abuf.h -rw-r--r-- root/root 6545 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam2bcf.h -rw-r--r-- root/root 2030 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam_sample.h -rw-r--r-- root/root 5142 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bcftools.h -rw-r--r-- root/root 1876 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bcftools.pysam.h -rw-r--r-- root/root 2188 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bin.h -rw-r--r-- root/root 5330 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/call.h -rw-r--r-- root/root 1808 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/cols.h -rw-r--r-- root/root 77 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam/include/bcftools/config.h -rw-r--r-- root/root 1881 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/convert.h -rw-r--r-- root/root 1851 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/dbuf.h -rw-r--r-- root/root 2850 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/dist.h -rw-r--r-- root/root 2180 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/extsort.h -rw-r--r-- root/root 2409 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/filter.h -rw-r--r-- root/root 1561 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/gvcf.h -rw-r--r-- root/root 2781 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/hclust.h -rw-r--r-- root/root 2968 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/hex.h -rw-r--r-- root/root 3163 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/khash_str2str.h -rw-r--r-- root/root 7726 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/kheap.h -rw-r--r-- root/root 1619 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/kmin.h -rw-r--r-- root/root 62247 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/mw.h -rw-r--r-- root/root 4414 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/ploidy.h -rw-r--r-- root/root 3556 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/prob1.h -rw-r--r-- root/root 7544 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/rbuf.h -rw-r--r-- root/root 8680 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/regidx.h -rw-r--r-- root/root 2211 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/smpl_ilist.h -rw-r--r-- root/root 2278 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/str_finder.h -rw-r--r-- root/root 2722 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/tsv2vcf.h -rw-r--r-- root/root 55978 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/utlist.h -rw-r--r-- root/root 20775 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/variantkey.h -rw-r--r-- root/root 4311 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/vcfbuf.h -rw-r--r-- root/root 2438 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/bcftools/vcmp.h drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/lib/python3/dist-packages/pysam/include/samtools/ -rw-r--r-- root/root 1523 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/samtools/bam.h -rw-r--r-- root/root 1794 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/samtools/bam_ampliconclip.h -rw-r--r-- root/root 2059 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/include/samtools/bam_lpileup.h -rw-r--r-- root/root 2126 2022-10-28 13:13 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-rw-r--r-- root/root 145 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/version.py -rw-r--r-- root/root 93 2022-10-28 13:13 ./usr/lib/python3/dist-packages/pysam/version.pyi drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/share/ drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/share/doc/python3-pysam/ -rw-r--r-- root/root 2122 2023-03-22 05:39 ./usr/share/doc/python3-pysam/changelog.Debian.gz -rw-r--r-- root/root 2688 2022-12-31 16:55 ./usr/share/doc/python3-pysam/copyright drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/share/lintian/ drwxr-xr-x root/root 0 2023-03-22 05:39 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 211 2022-12-31 16:55 ./usr/share/lintian/overrides/python3-pysam +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 250340 Build-Time: 2814 Distribution: lunar-proposed Host Architecture: riscv64 Install-Time: 311 Job: python-pysam_0.20.0+ds-3build1.dsc Machine Architecture: riscv64 Package: python-pysam Package-Time: 3147 Source-Version: 0.20.0+ds-3build1 Space: 250340 Status: successful Version: 0.20.0+ds-3build1 -------------------------------------------------------------------------------- Finished at 2023-03-22T06:41:22Z Build needed 00:52:27, 250340k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25688808 Scanning for processes to kill in build PACKAGEBUILD-25688808 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25688808 Stopping target for build PACKAGEBUILD-25688808 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-25688808 Removing build PACKAGEBUILD-25688808