https://launchpad.net/ubuntu/+source/python-pysam/0.21.0+ds-1/+build/26335195 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos03-amd64-032 5.4.0-152-generic #169-Ubuntu SMP Tue Jun 6 22:23:09 UTC 2023 x86_64 Buildd toolchain package versions: launchpad-buildd_233~634~ubuntu20.04.1 python3-lpbuildd_233~634~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 24 Jun 11:24:53 ntpdate[4663]: adjust time server 10.211.37.1 offset 0.000266 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26335195 --image-type chroot /home/buildd/filecache-default/1fc1752c0976ad9eb0e621fd063fde252dab04e3 Creating target for build PACKAGEBUILD-26335195 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26335195 Starting target for build PACKAGEBUILD-26335195 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26335195 'deb http://ftpmaster.internal/ubuntu mantic main universe' 'deb http://ftpmaster.internal/ubuntu mantic-security main universe' 'deb http://ftpmaster.internal/ubuntu mantic-updates main universe' 'deb http://ftpmaster.internal/ubuntu mantic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-26335195 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26335195 Updating target for build PACKAGEBUILD-26335195 Get:1 http://ftpmaster.internal/ubuntu mantic InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu mantic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 Packages [1400 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe amd64 Packages [15.1 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5936 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 Packages [68.5 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [24.2 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 Packages [493 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [169 kB] Fetched 24.3 MB in 3s (7427 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 base-files bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils ca-certificates coreutils cpp cpp-12 dash debconf diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-12 gcc gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep hostname libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 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 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libfdisk1 libgcc-12-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgprofng0 libgssapi-krb5-2 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblzma5 libmd0 libmount1 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtsan2 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev logsave lsb-base lto-disabled-list mawk mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tar tzdata usrmerge util-linux util-linux-extra xz-utils zlib1g 138 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After this operation, 323 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt-dev amd64 1:4.4.35-1 [112 kB] Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6-dev amd64 2.37-0ubuntu2 [2092 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-dev-bin amd64 2.37-0ubuntu2 [20.0 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt1 amd64 1:4.4.35-1 [82.1 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 linux-libc-dev amd64 6.3.0-7.7 [1544 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6 amd64 2.37-0ubuntu2 [3179 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-bin amd64 2.37-0ubuntu2 [669 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-13-base amd64 13.1.0-6ubuntu1 [42.0 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-s1 amd64 13.1.0-6ubuntu1 [62.5 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main amd64 base-files amd64 13ubuntu1 [74.0 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 bash amd64 5.2.15-2ubuntu1 [795 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main amd64 bsdutils amd64 1:2.38.1-5ubuntu2 [91.5 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 coreutils amd64 9.1-1ubuntu2 [1407 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main amd64 liblzma5 amd64 5.4.1-0.2 [125 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcrypt20 amd64 1.10.1-3ubuntu1 [529 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++6 amd64 13.1.0-6ubuntu1 [772 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main amd64 libacl1 amd64 2.3.1-3 [16.4 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 libapparmor1 amd64 3.0.8-1ubuntu3 [46.3 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit-common all 1:3.0.9-1 [5142 B] Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap-ng0 amd64 0.8.3-1build2 [15.3 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit1 amd64 1:3.0.9-1 [46.0 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main amd64 libblkid1 amd64 2.38.1-5ubuntu2 [111 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap2 amd64 1:2.66-4ubuntu1 [29.4 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 libperl5.36 amd64 5.36.0-7ubuntu1 [4834 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 perl amd64 5.36.0-7ubuntu1 [235 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-base amd64 5.36.0-7ubuntu1 [1784 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-modules-5.36 all 5.36.0-7ubuntu1 [2984 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [742 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu4 [61.2 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 debconf all 1.5.82 [125 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main amd64 libssl3 amd64 3.0.9-1ubuntu1 [1901 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 libzstd1 amd64 1.5.4+dfsg2-5 [292 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 libkmod2 amd64 30+20221128-1ubuntu1 [49.5 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 libpcre2-8-0 amd64 10.42-1 [228 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 libselinux1 amd64 3.4-1build4 [78.1 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main amd64 libmount1 amd64 2.38.1-5ubuntu2 [121 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam0g amd64 1.5.2-6ubuntu1 [65.9 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 libseccomp2 amd64 2.5.4-1ubuntu3 [49.1 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd-sysv amd64 252.5-2ubuntu3 [11.5 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd amd64 252.5-2ubuntu3 [3002 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd-shared amd64 252.5-2ubuntu3 [1832 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main amd64 libargon2-1 amd64 0~20190702+dfsg-3 [20.3 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main amd64 libudev1 amd64 252.5-2ubuntu3 [150 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-2ubuntu1 [139 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main amd64 libuuid1 amd64 2.38.1-5ubuntu2 [32.7 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main amd64 libcryptsetup12 amd64 2:2.6.1-4ubuntu1 [243 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main amd64 libfdisk1 amd64 2.38.1-5ubuntu2 [144 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main amd64 libp11-kit0 amd64 0.24.1-2ubuntu1 [248 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main amd64 mount amd64 2.38.1-5ubuntu2 [114 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd0 amd64 252.5-2ubuntu3 [389 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 libapt-pkg6.0 amd64 2.7.1 [930 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main amd64 tar amd64 1.34+dfsg-1.2ubuntu1 [293 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg amd64 1.21.22ubuntu1 [1393 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main amd64 dash amd64 0.5.12-2ubuntu1 [88.2 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main amd64 diffutils amd64 1:3.8-4 [176 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main amd64 findutils amd64 4.9.0-4ubuntu1 [299 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main amd64 grep amd64 3.8-5 [160 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main amd64 hostname amd64 3.23+nmu1ubuntu1 [11.0 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-bin amd64 6.4-4 [185 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main amd64 sed amd64 4.9-1 [193 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main amd64 libsmartcols1 amd64 2.38.1-5ubuntu2 [59.5 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main amd64 util-linux-extra amd64 2.38.1-5ubuntu2 [83.8 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main amd64 util-linux amd64 2.38.1-5ubuntu2 [1075 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-base all 6.4-4 [23.3 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main amd64 sysvinit-utils amd64 3.06-4ubuntu1 [33.0 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main amd64 lsb-base all 11.6 [4606 B] Get:67 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 adduser all 3.134ubuntu1 [136 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgv amd64 2.2.40-1.1ubuntu1 [140 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main amd64 libgnutls30 amd64 3.7.9-2ubuntu1 [999 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main amd64 apt amd64 2.7.1 [1359 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules-bin amd64 1.5.2-6ubuntu1 [47.3 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules amd64 1.5.2-6ubuntu1 [284 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main amd64 logsave amd64 1.47.0-1ubuntu1 [14.2 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main amd64 libext2fs2 amd64 1.47.0-1ubuntu1 [212 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main amd64 e2fsprogs amd64 1.47.0-1ubuntu1 [598 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main amd64 libattr1 amd64 1:2.5.1-4 [12.4 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main amd64 libdebconfclient0 amd64 0.267ubuntu1 [7892 B] Get:78 http://ftpmaster.internal/ubuntu mantic/main amd64 libmd0 amd64 1.1.0-1 [26.9 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage-common all 3.4-1build4 [9852 B] Get:81 http://ftpmaster.internal/ubuntu mantic/main amd64 libsepol2 amd64 3.4-2.1 [301 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage2 amd64 3.4-1build4 [92.7 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main amd64 libncurses6 amd64 6.4-4 [112 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main amd64 libncursesw6 amd64 6.4-4 [147 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main amd64 libtinfo6 amd64 6.4-4 [103 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main amd64 usrmerge all 35ubuntu1 [58.2 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main amd64 libcom-err2 amd64 1.47.0-1ubuntu1 [14.5 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main amd64 libproc2-0 amd64 2:4.0.3-1ubuntu1 [55.9 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main amd64 libss2 amd64 1.47.0-1ubuntu1 [16.8 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main amd64 mawk amd64 1.3.4.20230525-1 [113 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/main amd64 procps amd64 2:4.0.3-1ubuntu1 [609 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main amd64 sensible-utils all 0.0.20 [19.6 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main amd64 openssl amd64 3.0.9-1ubuntu1 [1189 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main amd64 ca-certificates all 20230311ubuntu1 [152 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main amd64 libgssapi-krb5-2 amd64 1.20.1-2 [142 kB] Get:96 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5-3 amd64 1.20.1-2 [346 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5support0 amd64 1.20.1-2 [32.7 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main amd64 libk5crypto3 amd64 1.20.1-2 [81.1 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main amd64 readline-common all 8.2-1.3 [55.7 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main amd64 libreadline8 amd64 8.2-1.3 [151 kB] Get:101 http://ftpmaster.internal/ubuntu mantic/main amd64 libsqlite3-0 amd64 3.40.1-2 [660 kB] Get:102 http://ftpmaster.internal/ubuntu mantic/main amd64 tzdata all 2023c-4exp1ubuntu1 [271 kB] Get:103 http://ftpmaster.internal/ubuntu mantic/main amd64 xz-utils amd64 5.4.1-0.2 [270 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main amd64 advancecomp amd64 2.5-1 [180 kB] Get:105 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgprofng0 amd64 2.40.50.20230622-1ubuntu1 [902 kB] Get:106 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libctf0 amd64 2.40.50.20230622-1ubuntu1 [97.1 kB] Get:107 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libctf-nobfd0 amd64 2.40.50.20230622-1ubuntu1 [99.7 kB] Get:108 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.40.50.20230622-1ubuntu1 [2524 kB] Get:109 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libbinutils amd64 2.40.50.20230622-1ubuntu1 [631 kB] Get:110 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 binutils amd64 2.40.50.20230622-1ubuntu1 [18.7 kB] Get:111 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 binutils-common amd64 2.40.50.20230622-1ubuntu1 [252 kB] Get:112 http://ftpmaster.internal/ubuntu mantic/main amd64 libisl23 amd64 0.26-3 [741 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main amd64 libmpfr6 amd64 4.2.0-1 [352 kB] Get:114 http://ftpmaster.internal/ubuntu mantic/main amd64 g++-12 amd64 12.3.0-3ubuntu1 [12.1 MB] Get:115 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12 amd64 12.3.0-3ubuntu1 [21.6 MB] Get:116 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp-12 amd64 12.3.0-3ubuntu1 [10.7 MB] Get:117 http://ftpmaster.internal/ubuntu mantic/main amd64 libubsan1 amd64 13.1.0-6ubuntu1 [1104 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/main amd64 libstdc++-12-dev amd64 12.3.0-3ubuntu1 [2180 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main amd64 libgomp1 amd64 13.1.0-6ubuntu1 [142 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/main amd64 libitm1 amd64 13.1.0-6ubuntu1 [29.5 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main amd64 libatomic1 amd64 13.1.0-6ubuntu1 [10.4 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/main amd64 libasan8 amd64 13.1.0-6ubuntu1 [2827 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/main amd64 liblsan0 amd64 13.1.0-6ubuntu1 [1203 kB] Get:124 http://ftpmaster.internal/ubuntu mantic/main amd64 libquadmath0 amd64 13.1.0-6ubuntu1 [153 kB] Get:125 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-12-dev amd64 12.3.0-3ubuntu1 [2575 kB] Get:126 http://ftpmaster.internal/ubuntu mantic/main amd64 libtsan2 amd64 13.1.0-6ubuntu1 [2599 kB] Get:127 http://ftpmaster.internal/ubuntu mantic/main amd64 libcc1-0 amd64 13.1.0-6ubuntu1 [48.1 kB] Get:128 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12-base amd64 12.3.0-3ubuntu1 [42.7 kB] Get:129 http://ftpmaster.internal/ubuntu mantic/main amd64 g++ amd64 4:12.2.0-3ubuntu1 [1120 B] Get:130 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc amd64 4:12.2.0-3ubuntu1 [5160 B] Get:131 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp amd64 4:12.2.0-3ubuntu1 [27.8 kB] Get:132 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg-dev all 1.21.22ubuntu1 [1118 kB] Get:133 http://ftpmaster.internal/ubuntu mantic/main amd64 libdpkg-perl all 1.21.22ubuntu1 [247 kB] Get:134 http://ftpmaster.internal/ubuntu mantic/main amd64 lto-disabled-list all 41 [12.4 kB] Get:135 http://ftpmaster.internal/ubuntu mantic/main amd64 libfakeroot amd64 1.31-1.2 [32.0 kB] Get:136 http://ftpmaster.internal/ubuntu mantic/main amd64 fakeroot amd64 1.31-1.2 [60.1 kB] Get:137 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg amd64 2.2.40-1.1ubuntu1 [523 kB] Get:138 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgconf amd64 2.2.40-1.1ubuntu1 [96.3 kB] Get:139 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg-agent amd64 2.2.40-1.1ubuntu1 [216 kB] Get:140 http://ftpmaster.internal/ubuntu mantic/main amd64 pkgbinarymangler all 153 [16.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 111 MB in 14s (8143 kB/s) (Reading database ... 13093 files and directories currently installed.) 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-26335195 amd64 mantic-proposed -c chroot:build-PACKAGEBUILD-26335195 --arch=amd64 --dist=mantic-proposed --nolog -A python-pysam_0.21.0+ds-1.dsc Initiating build PACKAGEBUILD-26335195 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-152-generic #169-Ubuntu SMP Tue Jun 6 22:23:09 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos03-amd64-032.buildd +==============================================================================+ | python-pysam 0.21.0+ds-1 (amd64) Sat, 24 Jun 2023 11:25:27 +0000 | +==============================================================================+ Package: python-pysam Version: 0.21.0+ds-1 Source Version: 0.21.0+ds-1 Distribution: mantic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26335195/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-wxFIoV/resolver-IewSQD' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- python-pysam_0.21.0+ds-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/python-pysam-wxFIoV/python-pysam-0.21.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-wxFIoV' 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 [526 B] Fetched 1938 B in 0s (175 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following 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-installer python3-wheel 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. 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(Reading database ... 12590 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.4-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.4-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-2_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.4-1_amd64.deb ... Unpacking python3.11-minimal (3.11.4-1) ... Setting up libpython3.11-minimal:amd64 (3.11.4-1) ... Setting up libexpat1:amd64 (2.5.0-2) ... Setting up python3.11-minimal (3.11.4-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 12904 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.2-1_amd64.deb ... Unpacking python3-minimal (3.11.2-1) ... Selecting previously unselected package media-types. Preparing to unpack .../media-types_10.0.0_all.deb ... 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Setting up media-types (10.0.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libicu72:amd64 (72.1-3ubuntu2) ... Setting up bsdextrautils (2.38.1-5ubuntu2) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libpython3.11-stdlib:amd64 (3.11.4-1) ... Setting up libdebhelper-perl (13.11.4ubuntu3) ... Setting up libbrotli1:amd64 (1.0.9-2build8) ... Setting up libnghttp2-14:amd64 (1.54.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.15-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-1) ... Setting up autotools-dev (20220109.1) ... Setting up libexpat1-dev:amd64 (2.5.0-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-1) ... Setting up libssh-4:amd64 (0.10.5-2) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1ubuntu4) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libdeflate-dev:amd64 (1.15-1) ... Setting up tabix (1.17+ds-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libldap2:amd64 (2.6.3+dfsg-1~exp1ubuntu2) ... Setting up libpython3-stdlib:amd64 (3.11.2-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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 (3.11.4-1) ... Setting up libdw1:amd64 (0.188-2.1) ... Setting up gettext (0.21-12) ... Setting up libpython3.11:amd64 (3.11.4-1) ... Setting up libtool (2.4.7-5) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10ubuntu1) ... Setting up python3 (3.11.2-1) ... Setting up libcurl4-gnutls-dev:amd64 (7.88.1-10ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up python3-packaging (23.1-1) ... Setting up libpython3.11-dev:amd64 (3.11.4-1) ... Setting up cython3 (0.29.32-2ubuntu2) ... Setting up libjs-sphinxdoc (5.3.0-4) ... 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 (3.11.4-1) ... Setting up python3-pkg-resources (67.8.0-1) ... Setting up python3-distutils (3.11.4-1) ... Setting up dh-python (6.20230603) ... Setting up python3-more-itertools (9.1.1-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up libhts3:amd64 (1.17+ds-1) ... Setting up libpython3-dev:amd64 (3.11.2-1) ... Setting up python3-setuptools (67.8.0-1) ... Setting up python3-py (1.11.0-1) ... Setting up python3.11-dev (3.11.4-1) ... Setting up python3-pytest (7.3.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up bcftools (1.16-1) ... Setting up libhts-dev:amd64 (1.17+ds-1) ... Setting up python3-all (3.11.2-1) ... Setting up man-db (2.11.2-2) ... 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 (1.17-1) ... Setting up libpython3-all-dev:amd64 (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 (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-152-generic #169-Ubuntu SMP Tue Jun 6 22:23:09 UTC 2023 amd64 (x86_64) Toolchain package versions: binutils_2.40.50.20230622-1ubuntu1 dpkg-dev_1.21.22ubuntu1 g++-12_12.3.0-3ubuntu1 gcc-12_12.3.0-3ubuntu1 libc6-dev_2.37-0ubuntu2 libstdc++-12-dev_12.3.0-3ubuntu1 libstdc++6_13.1.0-6ubuntu1 linux-libc-dev_6.3.0-7.7 Package versions: adduser_3.134ubuntu1 advancecomp_2.5-1 apt_2.7.1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_13ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 bcftools_1.16-1 binutils_2.40.50.20230622-1ubuntu1 binutils-common_2.40.50.20230622-1ubuntu1 binutils-x86-64-linux-gnu_2.40.50.20230622-1ubuntu1 bsdextrautils_2.38.1-5ubuntu2 bsdutils_1:2.38.1-5ubuntu2 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:12.2.0-3ubuntu1 cpp-12_12.3.0-3ubuntu1 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_6.20230603 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.21.22ubuntu1 dpkg-dev_1.21.22ubuntu1 dwz_0.15-1 e2fsprogs_1.47.0-1ubuntu1 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-4ubuntu1 g++_4:12.2.0-3ubuntu1 g++-12_12.3.0-3ubuntu1 gcc_4:12.2.0-3ubuntu1 gcc-12_12.3.0-3ubuntu1 gcc-12-base_12.3.0-3ubuntu1 gcc-13-base_13.1.0-6ubuntu1 gettext_0.21-12 gettext-base_0.21-12 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 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_3.0.8-1ubuntu3 libapt-pkg6.0_2.7.1 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-3 libasan8_13.1.0-6ubuntu1 libassuan0_2.5.5-5 libatomic1_13.1.0-6ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40.50.20230622-1ubuntu1 libblkid1_2.38.1-5ubuntu2 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_1:2.66-4ubuntu1 libcc1-0_13.1.0-6ubuntu1 libcom-err2_1.47.0-1ubuntu1 libcrypt-dev_1:4.4.35-1 libcrypt1_1:4.4.35-1 libcryptsetup12_2:2.6.1-4ubuntu1 libctf-nobfd0_2.40.50.20230622-1ubuntu1 libctf0_2.40.50.20230622-1ubuntu1 libcurl3-gnutls_7.88.1-10ubuntu1 libcurl4-gnutls-dev_7.88.1-10ubuntu1 libdb5.3_5.3.28+dfsg2-1 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login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-1ubuntu1 lsb-base_11.6 lto-disabled-list_41 m4_1.4.19-3 make_4.3-4.1build1 man-db_2.11.2-2 mawk_1.3.4.20230525-1 media-types_10.0.0 mount_2.38.1-5ubuntu2 ncurses-base_6.4-4 ncurses-bin_6.4-4 openssl_3.0.9-1ubuntu1 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-7ubuntu1 perl-base_5.36.0-7ubuntu1 perl-modules-5.36_5.36.0-7ubuntu1 pinentry-curses_1.2.1-1ubuntu1 pkgbinarymangler_153 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_3.11.4-1 python3-iniconfig_1.1.1-2 python3-lib2to3_3.11.4-1 python3-minimal_3.11.2-1 python3-more-itertools_9.1.1-2 python3-packaging_23.1-1 python3-pkg-resources_67.8.0-1 python3-pluggy_1.0.0+repack-1 python3-py_1.11.0-1 python3-pytest_7.3.2-1 python3-setuptools_67.8.0-1 python3.11_3.11.4-1 python3.11-dev_3.11.4-1 python3.11-minimal_3.11.4-1 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 samtools_1.17-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 systemd_252.5-2ubuntu3 systemd-sysv_252.5-2ubuntu3 sysvinit-utils_3.06-4ubuntu1 tabix_1.17+ds-1 tar_1.34+dfsg-1.2ubuntu1 tzdata_2023c-4exp1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_35ubuntu1 util-linux_2.38.1-5ubuntu2 util-linux-extra_2.38.1-5ubuntu2 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: 0.21.0+ds-1 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: e9d39e3a4b5c5f12475fe2b51efdda3981a1f749 1455428 python-pysam_0.21.0+ds.orig.tar.xz 40dd6caa92ddc27654906ee313b533d8b49d37c8 10548 python-pysam_0.21.0+ds-1.debian.tar.xz Checksums-Sha256: d6126717f11e261ba3ad1fa683cf038f0af044b2c2efbf9be68ec7f8f5e791b5 1455428 python-pysam_0.21.0+ds.orig.tar.xz 26d33fcda34360d10473f77fcb16db55d5f3122392d37d0350cb776d2ede7ca3 10548 python-pysam_0.21.0+ds-1.debian.tar.xz Files: 3ac021fcf33679ba6bfc7c5ea2207056 1455428 python-pysam_0.21.0+ds.orig.tar.xz 646650ec643a2782c476fb05234468e8 10548 python-pysam_0.21.0+ds-1.debian.tar.xz Dgit: ebbf869260bc7f7f6f6b59d89c091bf85533ccec debian archive/debian/0.21.0+ds-1 https://git.dgit.debian.org/python-pysam -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmSV47oUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpSCA//RomBIpPJevUzMUR3uut4vIVe4wP7 03oyvaQPplb7ATN7AoOQ7JikxkDWDLIKfm4xuOlibNFE1r1clW4qV6mHJpx6srQx oyP0fy0u0a4ADCu1NTf0R7WJ586lKtbyKK/WhOWBpDcsdlvZ4LcnzUAD5/g38WXi jQxIdj9LgCV4l6Ie2t9XnXMJLEtx/ecVrqRNesJH04aFdqCFyHcnUiLKur7+Gixo W/acGHFGkvfL9UrCtnwLjfbrLKWjYWH3fzM3yUd6v4cL1S0GrtIAGJIZocojrzyu ZUPna/AyzkUnbmAGsSv6nghymwAB2KnKff17FN+wrzzgD+9dSdqKyFo6Oby2cE2I YMSc/ZjBH8bmuHO8zJoP0c406eejICw0FldzY5mvACAS0HfGBQvQw/ftgJW+XEPd 9QU0OA81rb/DWH0GxRlii7XlgCY3alKSEsoHabv0m/MDIlWYAlBFf5vzSGhlrLej sjOQVSkWAZC6lu89seoMY8DeFsT8cSEfxNYHNgh6oFZdXqIXr1bfBFAWUMT9t2z6 HqqRI6W19bxIMKPiO3GbYh801XM3K5qrUWoLTyWlLLIF8+2YiqM/NiqamWz6WUUM fs3hoYqq11hQnDU4i/5R/4qXss1HZEWQM2gchvD9gUSxrxQorDBGLKrNrjHFpU7N +O2wgoz0xwlzadk= =dFqp -----END PGP SIGNATURE----- gpgv: Signature made Fri Jun 23 18:26:02 2023 UTC gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pysam_0.21.0+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting python-pysam in /<> dpkg-source: info: unpacking python-pysam_0.21.0+ds.orig.tar.xz dpkg-source: info: unpacking python-pysam_0.21.0+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_remote.patch dpkg-source: info: applying clean_less dpkg-source: info: applying skip-test-on-32-bit.patch dpkg-source: info: applying typos.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-26335195 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26335195 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26335195 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 0.21.0+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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:275: 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-x86_64' 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 dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:275: 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 -O--buildsystem=pybuild I: pybuild base:275: /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/Pileup.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/version.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/samtools.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/bcftools.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/__init__.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 creating /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing requirements to pysam.egg-info/requires.txt writing top-level names to pysam.egg-info/top_level.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'pysam/libc*.c' warning: no files found matching 'win32/*.[ch]' warning: no files found matching 'htslib/LICENSE' warning: no files found matching 'htslib/README' warning: no files found matching '*.[ch]' under directory 'htslib' warning: no previously-included files found matching 'htslib/*config*.h' warning: no files found matching 'htslib/configure.ac' warning: no files found matching 'htslib/m4/*.m4' warning: no files found matching 'htslib/*.in' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/version.sh' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/*.mk' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/cbcftools_util.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/csamtools_util.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/htslib_util.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/htslib_util.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignedsegment.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignedsegment.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignedsegment.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignmentfile.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignmentfile.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcf.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcf.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcf.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcftools.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcftools.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcftools.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbgzf.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbgzf.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcfaidx.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcfaidx.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcfaidx.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libchtslib.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libchtslib.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libchtslib.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamfile.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamfile.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamfile.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamtools.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamtools.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamtools.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabix.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabix.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabix.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabixproxies.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabixproxies.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcutils.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcutils.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcutils.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcvcf.pxd -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcvcf.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcvcf.pyx -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/py.typed -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/pysam_stream.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/pysam_util.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/pysam_util.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/version.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/version.pyi -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam creating /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/LICENSE -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/README -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/amplicon_stats.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam2depth.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_addrprg.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> /<>/.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/bam_aux.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_cat.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_color.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_consensus.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_fastq.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_flags.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_import.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_index.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> /<>/.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/bam_markdup.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_mate.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_md.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> /<>/.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/bam_plcmd.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_quickcheck.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_reheader.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_rmdup.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_rmdupse.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_samples.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_sort.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_split.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_stat.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bamshuf.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bamtk.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bedcov.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bedidx.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> /<>/.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/coverage.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/coverage.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/cram_size.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/cut_target.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/dict.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/dict.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/faidx.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/faidx.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/padding.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/padding.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/phase.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/phase.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/reference.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/reference.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/reset.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/reset.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sam_opts.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> /<>/.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/sam_utils.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sam_utils.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sam_view.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sample.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sample.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/sample.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/samtools.pysam.c -> /<>/.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/splaysort.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/stats.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/stats.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/stats_isize.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> /<>/.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/tmp_file.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> /<>/.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/version.sh -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools creating /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/lz4 copying samtools/config.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools creating /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/HMM.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/LICENSE -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/README -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/abuf.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/abuf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> /<>/.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/bcftools.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> /<>/.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/bin.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/bin.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/ccall.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/cigar_state.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/cols.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/cols.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/consensus.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/convert.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/csq.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/dbuf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/dist.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/dist.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/em.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/em.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/extsort.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/extsort.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/filter.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/gvcf.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/hclust.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> /<>/.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/khash_str2str.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/kmin.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/main.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/main.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/mcall.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/mpileup.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/ploidy.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/prob1.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/prob1.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/read_consensus.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/read_consensus.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/regidx.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/reheader.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> /<>/.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/str_finder.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> /<>/.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/tabix.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.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/variantkey.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfannotate.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfcall.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfcnv.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfconcat.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfconvert.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcffilter.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfhead.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfindex.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfisec.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfmerge.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfnorm.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfplugin.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfquery.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfroh.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfsom.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfsort.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfstats.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfview.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcmp.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/version.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/version.c.pysam.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/version.sh -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c cythoning pysam/libcutils.pyx to pysam/libcutils.c cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c warning: pysam/libcalignmentfile.pyx:2572:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2577:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2582:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2621:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2626:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2631:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c cythoning pysam/libctabix.pyx to pysam/libctabix.c cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c cythoning pysam/libcbcf.pyx to pysam/libcbcf.c cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c cythoning pysam/libcvcf.pyx to pysam/libcvcf.c warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libchtslib' extension creating build creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/pysam x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/htslib_util.o build/temp.linux-x86_64-cpython-311/pysam/libchtslib.o -L/<>/pysam -L/usr/lib/x86_64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-cpython-311/samtools creating build/temp.linux-x86_64-cpython-311/samtools/lz4 x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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/cram_size.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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/reset.c.pysam.c -o build/temp.linux-x86_64-cpython-311/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/libcsamtools.o build/temp.linux-x86_64-cpython-311/samtools/amplicon_stats.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_consensus.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_samples.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/consensus_pileup.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/coverage.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/cram_size.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/dict.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/faidx.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/lz4/lz4.o build/temp.linux-x86_64-cpython-311/samtools/padding.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/phase.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/reference.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/reset.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/sample.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/samtools.pysam.o build/temp.linux-x86_64-cpython-311/samtools/stats.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-cpython-311/samtools/tmp_file.c.pysam.o -L/<>/pysam -L/usr/lib/x86_64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-x86_64-cpython-311/bcftools x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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_iaux.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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/read_consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-311/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-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) | ^~~~~~ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/abuf.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bcftools.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/bin.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/cols.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/convert.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/csq.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/dist.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/em.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/extsort.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/filter.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/main.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/read_consensus.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/str_finder.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfhead.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-cpython-311/bcftools/version.c.pysam.o build/temp.linux-x86_64-cpython-311/pysam/libcbcftools.o -L/<>/pysam -L/usr/lib/x86_64-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/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN 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 | ^ /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) | ^ building 'pysam.libcutils' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/libcutils.o build/temp.linux-x86_64-cpython-311/pysam/pysam_util.o -L/<>/pysam -L/usr/lib/x86_64-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/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -lcsamtools.cpython-311-x86_64-linux-gnu -lcbcftools.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-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:28594:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28594 | (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:14277:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14277 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/libcalignmentfile.o -L/<>/pysam -L/usr/lib/x86_64-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/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/libcsamfile.o -L/<>/pysam -L/usr/lib/x86_64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-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:14351:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14351 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/libcalignedsegment.o -L/<>/pysam -L/usr/lib/x86_64-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/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libctabix.c -o build/temp.linux-x86_64-cpython-311/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/libctabix.o -L/<>/pysam -L/usr/lib/x86_64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/libcfaidx.o -L/<>/pysam -L/usr/lib/x86_64-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/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-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:67259:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 67259 | (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:66984:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66984 | (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:72118:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72118 | (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:35330:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35330 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:35356:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35356 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/libcbcf.o -L/<>/pysam -L/usr/lib/x86_64-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/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-cpython-311/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/libcbgzf.o -L/<>/pysam -L/usr/lib/x86_64-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/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-cpython-311/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/libctabixproxies.o -L/<>/pysam -L/usr/lib/x86_64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -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-x86_64-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.0’: pysam/libcvcf.c:25769:15: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 25769 | __pyx_t_8 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:20201:10: note: ‘__pyx_v_qual’ was declared here 20201 | double __pyx_v_qual; | ^~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pysam/libcvcf.o -L/<>/pysam -L/usr/lib/x86_64-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/x86_64-linux-gnu -lz -lhts -lchtslib.cpython-311-x86_64-linux-gnu -lcutils.cpython-311-x86_64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Entering directory '/<>' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/<>/tests/pysam_data' samtools faidx ex1.fa samtools view --no-PG -bo ex1.bam -t ex1.fa.fai ex1.sam.gz samtools mpileup -f ex1.fa ex1.bam | gzip > ex1.pileup.gz [mpileup] 1 samples in 1 input files gunzip < ex1.sam.gz > ex1.sam samtools index ex1.bam samtools view --no-PG -h ex1.bam | gzip > ex2.sam.gz gunzip < ex2.sam.gz > ex2.sam samtools view --no-PG -bo ex2.bam ex2.sam samtools index ex2.bam samtools calmd --no-PG --output-fmt BAM ex2.bam ex1.fa > with_md.sam.gz [bam_fillmd1] different NM for read 'EAS139_11:7:46:695:738': 3 -> 8 [bam_fillmd1] different NM for read 'EAS218_4:1:48:9:409': 0 -> 5 [bam_fillmd1] different NM for read 'B7_591:7:200:192:373': 0 -> 5 [bam_fillmd1] different NM for read 'EAS56_65:1:163:846:223': 0 -> 5 [bam_fillmd1] different NM for read 'EAS114_30:7:283:799:560': 0 -> 5 [bam_fillmd1] different NM for read 'B7_595:4:84:802:737': 0 -> 4 [bam_fillmd1] different NM for read 'EAS51_66:5:308:400:602': 0 -> 3 [bam_fillmd1] different NM for read 'EAS54_81:2:285:367:932': 0 -> 3 [bam_fillmd1] different NM for read 'EAS114_39:1:70:147:84': 0 -> 3 [bam_fillmd1] different NM for read 'EAS56_53:1:124:243:35': 2 -> 5 [bam_fillmd1] different NM for read 'EAS1_103:2:226:302:758': 2 -> 3 [bam_fillmd1] different NM for read 'EAS114_28:6:175:705:982': 1 -> 0 [bam_fillmd1] different NM for read 'EAS51_64:4:179:389:585': 7 -> 8 [bam_fillmd1] different NM for read 'B7_589:1:122:337:968': 3 -> 2 [bam_fillmd1] different NM for read 'B7_610:4:15:805:420': 4 -> 5 [bam_fillmd1] different NM for read 'B7_591:2:279:124:41': 2 -> 4 [bam_fillmd1] different NM for read 'EAS112_32:8:89:254:332': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:7:103:731:697': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_11:2:71:83:58': 0 -> 2 [bam_fillmd1] different NM for read 'EAS192_3:4:63:5:870': 0 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:29:1822:1881': 0 -> 2 [bam_fillmd1] different NM for read 'EAS188_7:3:15:568:42': 2 -> 1 [bam_fillmd1] different NM for read 'EAS1_95:4:176:971:874': 0 -> 1 [bam_fillmd1] different NM for read 'EAS1_99:1:34:649:318': 3 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:4:61:346:384': 3 -> 4 [bam_fillmd1] different NM for read 'B7_597:6:20:592:496': 0 -> 1 [bam_fillmd1] different NM for read 'B7_597:4:38:999:463': 2 -> 1 [bam_fillmd1] different NM for read 'EAS114_28:5:23:944:377': 0 -> 3 [bam_fillmd1] different NM for read 'EAS219_1:3:90:219:528': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_108:5:89:942:84': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:6:159:493:275': 0 -> 5 [bam_fillmd1] different NM for read 'EAS139_11:1:81:1019:558': 0 -> 5 [bam_fillmd1] different NM for read 'EAS51_62:7:162:195:761': 0 -> 4 [bam_fillmd1] different NM for read 'B7_597:3:115:646:430': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:243:209:110': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_108:2:266:994:429': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:5:32:461:154': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:6:7:492:1088': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_95:6:174:650:125': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:6:89:457:591': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_39:2:38:670:564': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_7:4:92:693:228': 1 -> 6 [bam_fillmd1] different NM for read 'EAS218_1:4:61:1369:440': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_26:4:123:1001:580': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_39:4:10:1312:1558': 0 -> 4 [bam_fillmd1] different NM for read 'EAS220_1:8:45:178:1321': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_59:5:125:137:58': 0 -> 4 [bam_fillmd1] different NM for read 'EAS192_3:3:285:349:797': 1 -> 5 [bam_fillmd1] different NM for read 'EAS114_45:5:56:1757:1319': 0 -> 4 [bam_fillmd1] different NM for read 'B7_591:3:291:404:199': 0 -> 4 [bam_fillmd1] different NM for read 'EAS54_65:7:159:253:353': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_57:1:122:38:103': 0 -> 4 [bam_fillmd1] different NM for read 'EAS188_4:5:103:870:105': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:8:24:718:322': 3 -> 7 [bam_fillmd1] different NM for read 'EAS51_64:6:118:41:489': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_61:3:165:665:220': 0 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:238:803:383': 0 -> 4 [bam_fillmd1] different NM for read 'EAS1_105:3:232:364:583': 0 -> 3 [bam_fillmd1] different NM for read 'B7_595:2:29:729:70': 3 -> 4 [bam_fillmd1] different NM for read 'EAS114_30:6:220:809:850': 4 -> 6 [bam_fillmd1] different NM for read 'EAS54_65:2:264:157:150': 3 -> 5 [bam_fillmd1] different NM for read 'B7_595:8:26:242:35': 2 -> 1 [bam_fillmd1] different NM for read 'B7_610:7:34:144:868': 4 -> 5 [bam_fillmd1] different NM for read 'B7_597:8:147:360:141': 1 -> 2 [bam_fillmd1] different NM for read 'EAS139_19:2:82:154:1333': 0 -> 4 [bam_fillmd1] different NM for read 'EAS56_63:3:41:468:459': 0 -> 3 [bam_fillmd1] different NM for read 'EAS1_97:4:274:287:423': 0 -> 1 [bam_fillmd1] different NM for read 'EAS114_30:2:303:428:326': 0 -> 1 [bam_fillmd1] different NM for read 'EAS54_71:8:105:854:975': 0 -> 3 gunzip < with_md.sam.gz > with_md.sam samtools view --no-PG -bo with_md.bam with_md.sam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated samtools index with_md.bam samtools view --no-PG -bu -o uncompressed.bam ex2.sam samtools view --no-PG -bo MM-chebi.bam MM-chebi.sam samtools view --no-PG -bo MM-double.bam MM-double.sam samtools view --no-PG -bo MM-multi.bam MM-multi.sam samtools view --no-PG -bo MM-orient.bam MM-orient.sam samtools view --no-PG -bo ex10.bam ex10.sam samtools view --no-PG -bo ex3.bam ex3.sam samtools view --no-PG -bo ex4.bam ex4.sam samtools view --no-PG -bo ex5.bam ex5.sam samtools view --no-PG -bo ex6.bam ex6.sam samtools view --no-PG -bo ex8.bam ex8.sam samtools view --no-PG -bo ex9_fail.bam ex9_fail.sam samtools view --no-PG -bo ex9_nofail.bam ex9_nofail.sam samtools view --no-PG -bo ex_spliced.bam ex_spliced.sam samtools view --no-PG -bo example_aligned_pairs.bam example_aligned_pairs.sam samtools view --no-PG -bo example_btag.bam example_btag.sam samtools view --no-PG -bo example_dash_in_chr.bam example_dash_in_chr.sam samtools view --no-PG -bo example_empty_header.bam example_empty_header.sam samtools view --no-PG -bo example_empty_with_header.bam example_empty_with_header.sam samtools view --no-PG -bo example_reverse_complement.bam example_reverse_complement.sam touch tmp.list samtools view --no-PG -bo example_unmapped_reads_no_sq.bam -t tmp.list example_unmapped_reads_no_sq.sam rm -f tmp.list samtools view --no-PG -bo issue100.bam issue100.sam samtools view --no-PG -bo rg_with_tab.bam rg_with_tab.sam samtools view --no-PG -bo softclip.bam softclip.sam samtools view --no-PG -bo tag_bug.bam tag_bug.sam samtools view --no-PG -bo test_mapped_unmapped.bam test_mapped_unmapped.sam samtools view --no-PG -bo test_query_position.bam test_query_position.sam samtools view --no-PG -bo test_unaligned.bam test_unaligned.sam samtools index MM-chebi.bam samtools index MM-double.bam samtools index MM-multi.bam samtools index MM-orient.bam samtools index ex10.bam samtools index ex3.bam samtools index ex4.bam samtools index ex5.bam samtools index ex6.bam samtools index ex8.bam samtools index ex9_fail.bam samtools index ex9_nofail.bam samtools index ex_spliced.bam samtools index example_aligned_pairs.bam samtools index example_btag.bam samtools index example_dash_in_chr.bam samtools index example_empty_header.bam samtools index example_empty_with_header.bam samtools index example_reverse_complement.bam samtools index example_unmapped_reads_no_sq.bam samtools index issue100.bam samtools index rg_with_tab.bam samtools index softclip.bam samtools index tag_bug.bam samtools index test_mapped_unmapped.bam samtools index test_query_position.bam samtools index test_unaligned.bam samtools view --no-PG -Co ex1.cram -T ex1.fa ex1.sam samtools view --no-PG -Co ex2.cram -T ex1.fa ex2.sam samtools view --no-PG -Co ex3.cram -T ex1.fa ex3.sam samtools index ex1.cram samtools index ex2.cram samtools index ex3.cram cp ex1.bam example_bai.bam samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai dd if=ex2.bam of=ex2_truncated.bam bs=$((`wc -c < ex2.bam`-512)) count=1 1+0 records in 1+0 records out 122292 bytes (122 kB, 119 KiB) copied, 0.000202972 s, 603 MB/s (bgzip -d < ex2.bam; printf '\37\0\0\0\1\0\0\0') | bgzip > ex2_corrupt.bam grep "^@" ex2.sam | samtools view --no-PG -bo empty.bam - samtools index empty.bam cp ex1.bam explicit_index.bam cp ex1.cram explicit_index.cram gzip < faidx_empty_seq.fq > faidx_empty_seq.fq.gz bgzip < ex1.fa > ex1.fa.gz samtools faidx ex1.fa.gz cp ex1.bam ex1_csi.bam samtools index -c ex1_csi.bam touch all.stamp rm with_md.sam make[2]: Leaving directory '/<>/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make all make[2]: Entering directory '/<>/tests/cbcf_data' bgzip < example_vcf40.vcf > example_vcf40.vcf.gz tabix -p vcf example_vcf40.vcf.gz # create tbi index bcftools index example_vcf40.vcf.gz # create csi index bgzip < example_vcf42.vcf > example_vcf42.vcf.gz tabix -p vcf example_vcf42.vcf.gz # create tbi index bcftools index example_vcf42.vcf.gz # create csi index bgzip < example_vcf42_only_header.vcf > example_vcf42_only_header.vcf.gz tabix -p vcf example_vcf42_only_header.vcf.gz # create tbi index bcftools index example_vcf42_only_header.vcf.gz # create csi index bgzip < example_vcf42_withcontigs.vcf > example_vcf42_withcontigs.vcf.gz tabix -p vcf example_vcf42_withcontigs.vcf.gz # create tbi index bcftools index example_vcf42_withcontigs.vcf.gz # create csi index bgzip < example_vcf43.vcf > example_vcf43.vcf.gz tabix -p vcf example_vcf43.vcf.gz # create tbi index bcftools index example_vcf43.vcf.gz # create csi index bgzip < example_vcf43_with_utf8.vcf > example_vcf43_with_utf8.vcf.gz tabix -p vcf example_vcf43_with_utf8.vcf.gz # create tbi index bcftools index example_vcf43_with_utf8.vcf.gz # create csi index bgzip < gnomad.vcf > gnomad.vcf.gz tabix -p vcf gnomad.vcf.gz # create tbi index bcftools index gnomad.vcf.gz # create csi index bgzip < gnomad_fixed.vcf > gnomad_fixed.vcf.gz tabix -p vcf gnomad_fixed.vcf.gz # create tbi index bcftools index gnomad_fixed.vcf.gz # create csi index bgzip < missing_genotypes.vcf > missing_genotypes.vcf.gz tabix -p vcf missing_genotypes.vcf.gz # create tbi index bcftools index missing_genotypes.vcf.gz # create csi index bcftools view -O b example_vcf40.vcf.gz -o example_vcf40.bcf bcftools index example_vcf40.bcf bcftools view -O b example_vcf42.vcf.gz -o example_vcf42.bcf bcftools index example_vcf42.bcf bcftools view -O b example_vcf42_only_header.vcf.gz -o example_vcf42_only_header.bcf bcftools index example_vcf42_only_header.bcf bcftools view -O b example_vcf42_withcontigs.vcf.gz -o example_vcf42_withcontigs.bcf bcftools index example_vcf42_withcontigs.bcf bcftools view -O b example_vcf43.vcf.gz -o example_vcf43.bcf bcftools index example_vcf43.bcf bcftools view -O b example_vcf43_with_utf8.vcf.gz -o example_vcf43_with_utf8.bcf bcftools index example_vcf43_with_utf8.bcf bcftools view -O b gnomad.vcf.gz -o gnomad.bcf bcftools index gnomad.bcf bcftools view -O b gnomad_fixed.vcf.gz -o gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools index gnomad_fixed.bcf [W::bcf_hdr_check_sanity] PL should be declared as Number=G bcftools view -O b missing_genotypes.vcf.gz -o missing_genotypes.bcf bcftools index missing_genotypes.bcf touch all.stamp make[2]: Leaving directory '/<>/tests/cbcf_data' dh_auto_test I: pybuild base:275: cd /<>/.pybuild/cpython3_3.11_pysam/build; python3.11 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.11.4, pytest-7.3.2, pluggy-1.0.0+repack -- /usr/bin/python3.11 cachedir: .pytest_cache rootdir: /<> configfile: setup.cfg collecting ... collected 949 items tests/AlignedSegment_test.py::TestAlignedSegment::testBlocks PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testCompare PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testEmpty PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testFullReferencePositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testHashing PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testLargeRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testNoSequence PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testPositions PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testSettingTagInEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testStrOfEmptyRead PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdate2 PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateQual PASSED tests/AlignedSegment_test.py::TestAlignedSegment::testUpdateTlen PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_mapped_reads_are_updated PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_bin_values_for_unmapped_reads_ignore_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_equivalence_matches_only_and_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_hard_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_lowercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_match_mismatch PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_padding_with_seq PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_skip_reference PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_soft_clipping PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_uppercase_md PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_get_aligned_pairs_with_malformed_MD_tag PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_header_accessible PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_query_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_infer_read_length PASSED tests/AlignedSegment_test.py::TestAlignedSegment::test_query_length_is_limited PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestTidMapping::test_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestTidMapping::test_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestTidMapping::test_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_asterisk PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_be_set_to_none PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_reference_name_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_equal PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_to_missing_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_be_set_without_header PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_tid_can_not_be_set_to_unknown_chromosome PASSED tests/AlignedSegment_test.py::TestNextTidMapping::test_next_unmapped_tid_is_asterisk_in_output PASSED tests/AlignedSegment_test.py::TestCigar::testCigar PASSED tests/AlignedSegment_test.py::TestCigar::testCigarString PASSED tests/AlignedSegment_test.py::TestCigarStats::testStats PASSED tests/AlignedSegment_test.py::TestAlignedPairs::testReferenceBases PASSED tests/AlignedSegment_test.py::TestBaseModifications::testChebi PASSED tests/AlignedSegment_test.py::TestBaseModifications::testDouble PASSED tests/AlignedSegment_test.py::TestBaseModifications::testMulti PASSED tests/AlignedSegment_test.py::TestBaseModifications::testOrient PASSED tests/AlignedSegment_test.py::TestTags::testAddTags PASSED tests/AlignedSegment_test.py::TestTags::testAddTagsType PASSED tests/AlignedSegment_test.py::TestTags::testArrayTags PASSED tests/AlignedSegment_test.py::TestTags::testEmptyTag PASSED tests/AlignedSegment_test.py::TestTags::testLongTags PASSED tests/AlignedSegment_test.py::TestTags::testMDTagComplex PASSED tests/AlignedSegment_test.py::TestTags::testMDTagDeletions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagInsertions PASSED tests/AlignedSegment_test.py::TestTags::testMDTagMatchOnly PASSED tests/AlignedSegment_test.py::TestTags::testMDTagRefSkipping PASSED tests/AlignedSegment_test.py::TestTags::testMDTagSoftClipping PASSED tests/AlignedSegment_test.py::TestTags::testMissingTag PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegers PASSED tests/AlignedSegment_test.py::TestTags::testNegativeIntegersWrittenToFile [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp___enter___kl8jlx5znegative_integers.bam' PASSED tests/AlignedSegment_test.py::TestTags::testSetTag PASSED tests/AlignedSegment_test.py::TestTags::testTagParsing PASSED tests/AlignedSegment_test.py::TestTags::testTagsUpdatingFloat PASSED tests/AlignedSegment_test.py::TestCopy::testCopy PASSED tests/AlignedSegment_test.py::TestCopy::testDeepCopy PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_A PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_C PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_H PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_I PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_S PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_a PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_automated_type_detection PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_c PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_d PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_f PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_i PASSED tests/AlignedSegment_test.py::TestSetTagsGetTag::test_set_tag_with_s PASSED tests/AlignedSegment_test.py::TestEnums::test_cigar_enums_are_defined PASSED tests/AlignedSegment_test.py::TestEnums::test_sam_flags_are_defined PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_constructed_without_header PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_read_can_be_written_to_file PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_id_can_be_set PASSED tests/AlignedSegment_test.py::TestBuildingReadsWithoutHeader::test_reference_name_is_not_available PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_qualities_are_complemented PASSED tests/AlignedSegment_test.py::TestForwardStrandValues::test_sequence_is_complemented PASSED tests/AlignedSegment_test.py::TestExportImport::test_dict_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_with_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_string_export_import_without_tags PASSED tests/AlignedSegment_test.py::TestExportImport::test_to_string_without_alignment_file PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_dict PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_header PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_references_without_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderConstruction::test_header_constructed_from_text PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderSAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_contains_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_get_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_keys_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_len_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_setting_raises_error PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_values_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_name_mapping PASSED tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_text_access_works PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_qcismmo2' /<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_qcismmo2 PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_CRAM [E::cram_index_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_44hwdun7' /<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_44hwdun7 PASSED tests/AlignmentFileHeader_test.py::TestHeaderWriteRead::test_SAM /<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_c94u4h1_ PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_BAM [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_yhsqfss7' /<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_yhsqfss7 PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_CRAM [W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 2147483647 vs 1575 [E::cram_index_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_x_gvu6qr' /<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_x_gvu6qr PASSED tests/AlignmentFileHeader_test.py::TestHeaderLargeContigs::test_SAM /<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_write_f136ki9u PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelection::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_all_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_ignore_overlaps PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_base_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_ignore_orphans PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_mapping_quality_threshold PASSED tests/AlignmentFilePileup_test.py::TestPileupReadSelectionFastafile::test_samtools_stepper_redo_baq PASSED tests/AlignmentFilePileup_test.py::TestPileupQueryPosition::testPileup PASSED tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope SKIPPED tests/AlignmentFilePileup_test.py::TestPileupObjects::testPileupColumn PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testInverse PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateAll PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIteratePerContig PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateRanges PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumnBAM::testIterateTruncate PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testAccessOnClosedIterator PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStart PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testStr PASSED tests/AlignmentFilePileup_test.py::TestIteratorColumn2::testTruncate PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_depths_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_mapping_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_with_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_bases_without_reference_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_are_equal PASSED tests/AlignmentFilePileup_test.py::PileUpColumnTests::test_pileup_query_qualities_from_pileups_are_equal PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFetch::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFetch::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFilename::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFilename::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestBAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFile::testTags PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromFileNo::testTags PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFile::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARQueryLength [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigar [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARcigarstring [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARflag [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmapq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARmrnm [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARpos [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARqual [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARquery [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARrname [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testARseq [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testOpt [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPairedBools [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testPresentOptionalFields [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestCRAMFromFileNo::testTags [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARQueryLength PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigar PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARcigarstring PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARflag PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmapq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARmrnm PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARpos PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARqual PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARquery PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARrname PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testARseq PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testOpt PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPairedBools PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testPresentOptionalFields PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testRaises PASSED tests/AlignmentFile_test.py::BasicTestSAMFromStringIO::testTags PASSED tests/AlignmentFile_test.py::TestIO::testBAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testBAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithCSIIndex PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithShortBAI PASSED tests/AlignmentFile_test.py::TestIO::testBAMWithoutAlignedSegments PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2BAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testCRAM2SAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testEmptyBAM PASSED tests/AlignmentFile_test.py::TestIO::testEmptyWithHeaderBAM PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFile PASSED tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject PASSED tests/AlignmentFile_test.py::TestIO::testHead PASSED tests/AlignmentFile_test.py::TestIO::testOpenFromFilename PASSED tests/AlignmentFile_test.py::TestIO::testReadBamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadSamWithoutTargetNames PASSED tests/AlignmentFile_test.py::TestIO::testReadingFromFileWithoutIndex [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testReadingFromFileWithoutIndex_tlq03k8atmp_ex2.bam' PASSED tests/AlignmentFile_test.py::TestIO::testSAM2BAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2CRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAM PASSED tests/AlignmentFile_test.py::TestIO::testSAM2SAMWithoutHeader PASSED tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile PASSED tests/AlignmentFile_test.py::TestIO::test_accessing_attributes_in_closed_file_raises_errors PASSED tests/AlignmentFile_test.py::TestIO::test_fail_read_sam_without_header PASSED tests/AlignmentFile_test.py::TestIO::test_fail_when_reading_unformatted_files PASSED tests/AlignmentFile_test.py::TestIO::test_fetch_by_tid PASSED tests/AlignmentFile_test.py::TestIO::test_header_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_with_header_without_header_check PASSED tests/AlignmentFile_test.py::TestIO::test_pass_read_sam_without_header_with_refs PASSED tests/AlignmentFile_test.py::TestIO::test_reference_name_available_after_closing_file PASSED tests/AlignmentFile_test.py::TestIO::test_write_bam_to_unknown_path_fails [E::hts_open_format] Failed to open file "missing_directory/new_file.bam" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAutoDetect::testBAM PASSED tests/AlignmentFile_test.py::TestAutoDetect::testCRAM [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestAutoDetect::testSAM PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIteratePerContig PASSED tests/AlignmentFile_test.py::TestIteratorRowBAM::testIterateRanges PASSED tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAM::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIteratePerContig [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestIteratorRowCRAMWithReferenceFilename::testIterateRanges [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestFloatTagBug::testFloatTagBug PASSED tests/AlignmentFile_test.py::TestLargeFieldBug::testLargeFileBug PASSED tests/AlignmentFile_test.py::TestClipping::testClipping PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_bam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_from_sam_with_until_eof_reads_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads PASSED tests/AlignmentFile_test.py::TestUnmappedReadsRetrieval::test_fetch_with_asterisk_only_returns_unmapped_reads_by_contig PASSED tests/AlignmentFile_test.py::TestContextManager::testManager PASSED tests/AlignmentFile_test.py::TestMultiThread::testSingleThreadEqualsMultithread [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_6pd4dm5ltmp_single.bam' [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithread_jm3ehjsbtmp_multi.bam' PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBackwardsOrderOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testBadContig PASSED tests/AlignmentFile_test.py::TestExceptions::testMeaninglessCrap PASSED tests/AlignmentFile_test.py::TestExceptions::testMissingFile [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.bam" : No such file or directory [E::hts_open_format] Failed to open file "exdoesntexist.sam" : No such file or directory PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeLargeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeNewFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testOutOfRangeNegativeOldFormat PASSED tests/AlignmentFile_test.py::TestExceptions::testZeroToZero PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenBamAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsBam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenFastaAsSam PASSED tests/AlignmentFile_test.py::TestWrongFormat::testOpenSamAsBam PASSED tests/AlignmentFile_test.py::TestRegionParsing::test_dash_in_chr PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile PASSED tests/AlignmentFile_test.py::TestDeNovoConstruction::test_pass_if_reads_binary_equal PASSED tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader PASSED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_in_header [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/0example_no_seq_in_header.bam' PASSED tests/AlignmentFile_test.py::TestEmptyHeader::test_bam_without_seq_with_null_bytes_in_header [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/0example_no_seq_in_header_null_bytes.bam' PASSED tests/AlignmentFile_test.py::TestMismatchingHeader::testMismatchingHeader PASSED tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 PASSED tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBamIterator [W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/ex2_truncated.bam' [E::bgzf_read_block] Failed to read BGZF block data at offset 105180 expected 17578 bytes; hread returned 17094 [E::bgzf_read] Read block operation failed with error 4 after 0 of 4 bytes PASSED tests/AlignmentFile_test.py::TestCorruptBAM::testCorruptBamIterator [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/pysam_data/ex2_corrupt.bam' PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagSam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadTags PASSED tests/AlignmentFile_test.py::TestBTagBam::testReadWriteTags PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetch PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchUntilEOF PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionFalseTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueFalse PASSED tests/AlignmentFile_test.py::TestDoubleFetchBAM::testDoubleFetchWithRegionTrueTrue PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAM::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetch [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchUntilEOF [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionFalseTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueFalse [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestDoubleFetchCRAMWithReference::testDoubleFetchWithRegionTrueTrue [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/b6853ffe730ece50076db834dea18e3b": Connection refused PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetch PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testFetchAll PASSED tests/AlignmentFile_test.py::TestRemoteFileHTTP::testView PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testBAM PASSED tests/AlignmentFile_test.py::TestLargeOptValues::testSAM PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_counts_as_expected PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_nofilter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_quality_filter PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_all PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_read_callback PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_with_coordinates_works PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_without_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_count_coverage_wrong_coordinates_fails PASSED tests/AlignmentFile_test.py::TestCountCoverage::test_counting_the_same_region_works PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_all PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_first PASSED tests/AlignmentFile_test.py::TestFindIntrons::test_total PASSED tests/AlignmentFile_test.py::TestLogging::testFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail1 PASSED tests/AlignmentFile_test.py::TestLogging::testNoFail2 PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testCount PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testIndexStats PASSED tests/AlignmentFile_test.py::TestAlignmentFileUtilityFunctions::testMate PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct PASSED tests/AlignmentFile_test.py::TestMappedUnmapped::test_counts_of_mapped_and_unmapped_are_correct_per_chromosome PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testIndex PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testSort [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestSamtoolsProxy::testView [E::hts_open_format] Failed to open file "missing_file" : No such file or directory PASSED tests/AlignmentFile_test.py::TestAlignmentFileIndex::testIndex PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testExplicitIndexCRAM PASSED tests/AlignmentFile_test.py::TestExplicitIndex::testRemoteExplicitIndexBAM PASSED tests/AlignmentFile_test.py::TestVerbosity::testVerbosity PASSED tests/AlignmentFile_test.py::TestSanityCheckingBAM::test_empty_read_gives_value_error PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_bam [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_check_read_jsvsgz30tmp_largecigar.bam' PASSED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_cram SKIPPED tests/AlignmentFile_test.py::TestLargeCigar::test_reading_writing_sam PASSED tests/StreamFiledescriptors_test.py::StreamTest::test_samtools_processing SKIPPED tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCF PASSED tests/VariantFile_test.py::TestMissingGenotypes::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamples::testVCF PASSED tests/VariantFile_test.py::TestMissingSamples::testVCFGZ PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCF [W::bcf_hdr_check_sanity] PL should be declared as Number=G PASSED tests/VariantFile_test.py::TestMissingSamplesFixed::testVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testDetectBCF PASSED tests/VariantFile_test.py::TestOpening::testDetectVCF [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestOpening::testDetectVCFGZ PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCF PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFFromPath PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFGZWithoutIndex PASSED tests/VariantFile_test.py::TestOpening::testEmptyFileVCFOnlyHeader PASSED tests/VariantFile_test.py::TestOpening::testMissingFile [E::hts_open_format] Failed to open file "missing_file.vcf" : No such file or directory PASSED tests/VariantFile_test.py::TestOpening::testMissingFileVCFGZ [E::hts_open_format] Failed to open file "missing_file.vcf.gz" : No such file or directory PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_prebuilt_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_bcf_with_tbi_index_will_produce_csi PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_csi_index PASSED tests/VariantFile_test.py::TestIndexFormatsVCF::test_vcf_with_tbi_index PASSED tests/VariantFile_test.py::TestHeader::testIterator PASSED tests/VariantFile_test.py::TestHeader::testStr PASSED tests/VariantFile_test.py::TestParsing::testAlleles PASSED tests/VariantFile_test.py::TestParsing::testAllelesVariantTypes PASSED tests/VariantFile_test.py::TestParsing::testAlt PASSED tests/VariantFile_test.py::TestParsing::testChrom PASSED tests/VariantFile_test.py::TestParsing::testChromFromPath PASSED tests/VariantFile_test.py::TestParsing::testFilter PASSED tests/VariantFile_test.py::TestParsing::testFormat PASSED tests/VariantFile_test.py::TestParsing::testId PASSED tests/VariantFile_test.py::TestParsing::testInfo PASSED tests/VariantFile_test.py::TestParsing::testPos PASSED tests/VariantFile_test.py::TestParsing::testQual PASSED tests/VariantFile_test.py::TestParsing::testRef PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleleIndices PASSED tests/VariantFile_test.py::TestParsing::testSampleAlleles PASSED tests/VariantFile_test.py::TestParsing::testSampleFormats PASSED tests/VariantFile_test.py::TestParsing::testStart PASSED tests/VariantFile_test.py::TestParsing::testStop PASSED tests/VariantFile_test.py::TestIndexFilename::testOpen PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testBase PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionFromCopy PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithLines PASSED tests/VariantFile_test.py::TestConstructionVCFGZWithoutContigs::testConstructionWithRecords PASSED tests/VariantFile_test.py::TestSettingRecordValues::testBase PASSED tests/VariantFile_test.py::TestSettingRecordValues::testGenotype [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) (0, 0) PASSED tests/VariantFile_test.py::TestSettingRecordValues::testSetQual [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestMultiThreading::testNoMultiThreadingWithIgnoreTruncation PASSED tests/VariantFile_test.py::TestMultiThreading::testSingleThreadEqualsMultithreadResult [E::idx_find_and_load] Could not retrieve index file for '/<>/.pybuild/cpython3_3.11_pysam/build/tests/tmp/pysamtests_tmp_testSingleThreadEqualsMultithreadResult_l0cjv6xx.bcf' PASSED tests/VariantFile_test.py::TestSubsetting::testSubsetting PASSED tests/VariantFile_test.py::TestVCFVersions::test_all_records_can_be_fetched [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/VariantFile_test.py::TestUnicode::test_record_with_unicode PASSED tests/VariantRecord_test.py::test_ascii_annotation_can_be_added PASSED tests/VariantRecord_test.py::test_ascii_annotation_with_variable_length_can_be_added PASSED tests/VariantRecord_test.py::test_unicode_annotation_can_be_added PASSED tests/VariantRecord_test.py::test_set_sample_alleles PASSED tests/compile_test.py::test_bam PASSED tests/compile_test.py::test_gtf PASSED tests/faidx_test.py::TestFastaFile::testFetch PASSED tests/faidx_test.py::TestFastaFile::testFetchErrors PASSED tests/faidx_test.py::TestFastaFile::testLength PASSED tests/faidx_test.py::TestFastaFile::testOutOfRangeAccess PASSED tests/faidx_test.py::TestFastaFile::testSequenceLengths PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_and_contig_raises_exception PASSED tests/faidx_test.py::TestFastaFile::test_fetch_with_region_is_equivalent PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndex::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_abritrarily_named_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_with_explicit_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_open_file_without_index_succeeds PASSED tests/faidx_test.py::TestFastaFilePathIndexCompressed::test_raise_exception_if_index_is_missing PASSED tests/faidx_test.py::TestFastxFileFastq::testCounts PASSED tests/faidx_test.py::TestFastxFileFastq::testManager PASSED tests/faidx_test.py::TestFastxFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastq::testSequence PASSED tests/faidx_test.py::TestFastqFileFastq::testCounts PASSED tests/faidx_test.py::TestFastqFileFastq::testManager PASSED tests/faidx_test.py::TestFastqFileFastq::testMissingFile PASSED tests/faidx_test.py::TestFastqFileFastq::testSequence PASSED tests/faidx_test.py::TestFastxFileFasta::testCounts PASSED tests/faidx_test.py::TestFastxFileFasta::testManager PASSED tests/faidx_test.py::TestFastxFileFasta::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFasta::testSequence PASSED tests/faidx_test.py::TestFastxFileFastqStream::testCounts PASSED tests/faidx_test.py::TestFastxFileFastqStream::testManager PASSED tests/faidx_test.py::TestFastxFileFastqStream::testMissingFile PASSED tests/faidx_test.py::TestFastxFileFastqStream::testSequence PASSED tests/faidx_test.py::TestFastxFileWithEmptySequence::testIteration PASSED tests/faidx_test.py::TestRemoteFileFTP::testFTPView PASSED tests/faidx_test.py::TestRemoteFileFTP::test_sequence_lengths_are_available PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_can_be_created_from_scratch PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_comment_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_name_is_None PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_fail_if_quality_is_wrong_length PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_name_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_quality_can_be_modified PASSED tests/faidx_test.py::TestFastqRecord::test_fastx_record_sequence_can_be_modified PASSED tests/faidx_test.py::TestFastqProxy::test_fastq_proxy_instantiation_raises_error PASSED tests/linking_test.py::TestLinking::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithRpath::test_package_tests_pass SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_can_be_installed SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_fail_on_import SKIPPED tests/linking_test.py::TestLinkWithoutRpath::test_package_tests_pass_if_ld_library_path_set SKIPPED tests/samtools_test.py::SamtoolsTest::testStatements PASSED tests/samtools_test.py::SamtoolsTest::testUsage SKIPPED (skipping us...) tests/samtools_test.py::EmptyIndexTest::testEmptyIndex PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraArg PASSED tests/samtools_test.py::EmptyIndexTest::testEmptyIndexWithExtraFlag PASSED tests/samtools_test.py::TestReturnType::testReturnValueData PASSED tests/samtools_test.py::TestReturnType::testReturnValueString PASSED tests/samtools_test.py::StdoutTest::testDoubleCalling PASSED tests/samtools_test.py::StdoutTest::testSaveStdout PASSED tests/samtools_test.py::StdoutTest::testWithRedirectedStdout PASSED tests/samtools_test.py::StdoutTest::testWithoutRedirectedStdout PASSED tests/samtools_test.py::PysamTest::testStatements PASSED tests/samtools_test.py::PysamTest::testUsage SKIPPED (skipping usage...) tests/tabix_test.py::TestIndexing::test_indexing_to_custom_location_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_explict_columns_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_lineskipping_works PASSED tests/tabix_test.py::TestIndexing::test_indexing_with_preset_works PASSED tests/tabix_test.py::TestCompression::testCompression PASSED tests/tabix_test.py::TestCompression::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompression::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionSam::testCompression PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionSam::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionBed::testCompression PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionBed::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestCompressionVCF::testCompression PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetCompressed PASSED tests/tabix_test.py::TestCompressionVCF::testIndexPresetUncompressed PASSED tests/tabix_test.py::TestGZFile::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testAll PASSED tests/tabix_test.py::TestIterationWithoutComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithoutComments::testHeader PASSED tests/tabix_test.py::TestIterationWithoutComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithoutComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithoutComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithoutComments::testReopening PASSED tests/tabix_test.py::TestIterationWithComments::testAll PASSED tests/tabix_test.py::TestIterationWithComments::testGetContigs PASSED tests/tabix_test.py::TestIterationWithComments::testHeader PASSED tests/tabix_test.py::TestIterationWithComments::testInvalidIntervals PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig PASSED tests/tabix_test.py::TestIterationWithComments::testPerContig2 PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigFromStart PASSED tests/tabix_test.py::TestIterationWithComments::testPerContigToEnd PASSED tests/tabix_test.py::TestIterationWithComments::testPerInterval PASSED tests/tabix_test.py::TestIterationWithComments::testRegionStrings PASSED tests/tabix_test.py::TestIterationWithComments::testReopening PASSED tests/tabix_test.py::TestIterators::testClosedFile PASSED tests/tabix_test.py::TestIterators::testClosedFileIteration PASSED tests/tabix_test.py::TestIterators::testIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsGenericCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileCompressed::testIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFile PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testClosedFileIteration PASSED tests/tabix_test.py::TestIteratorsFileUncompressed::testIteration PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooFewFields PASSED tests/tabix_test.py::TestIterationMalformattedGTFFiles::testGTFTooManyFields PASSED tests/tabix_test.py::TestBed::testRead PASSED tests/tabix_test.py::TestBed::testWrite PASSED tests/tabix_test.py::TestUnicode::testFromTabix PASSED tests/tabix_test.py::TestUnicode::testFromVCF PASSED tests/tabix_test.py::TestVCFFromTabix::testRead PASSED tests/tabix_test.py::TestVCFFromTabix::testWrite PASSED tests/tabix_test.py::TestVCFFromVCF::testConnecting PASSED tests/tabix_test.py::TestVCFFromVCF::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_9::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_9::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_9::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_9::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_3::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_3::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_3::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_3::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_13::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_13::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_13::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_13::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_11::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_11::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_11::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_11::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_15::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_15::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_15::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_15::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_2::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_2::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_2::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_2::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_8::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_8::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_8::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_8::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_16::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_16::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_16::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_16::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_20::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_20::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_20::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_20::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_12::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_12::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_12::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_12::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_10::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_10::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_10::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_10::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_6::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_6::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_6::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_6::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_23::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_23::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_23::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_23::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_issue85::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_issue85::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_vcf_v42::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_vcf_v42::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_7::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_7::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_7::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_7::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_5::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_5::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_5::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_5::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_4::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_4::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_4::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_4::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_18::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_18::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_18::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_18::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_24::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_24::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_24::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_24::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_22::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_22::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_22::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_22::testParsing PASSED tests/tabix_test.py::VCFFromTabixTest_21::testRead PASSED tests/tabix_test.py::VCFFromTabixTest_21::testWrite PASSED tests/tabix_test.py::VCFFromVCFTest_21::testConnecting PASSED tests/tabix_test.py::VCFFromVCFTest_21::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile::testParsing [W::vcf_parse] Contig 'M' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_9::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_3::testParsing [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testConnecting [W::bcf_hrec_check] Invalid tag name: "1000g" [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" [W::bcf_hdr_check_sanity] GL should be declared as Number=G PASSED tests/tabix_test.py::TestVCFFromVariantFile_13::testParsing [W::bcf_hrec_check] Invalid tag name: "1000g" [W::bcf_hrec_check] Invalid tag name: "GT:GL:GQ:NR" [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'MMLQ' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17_gl000205_random' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr18' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr19' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr21' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr22' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000214' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000220' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrUn_gl000225' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chrX' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_11::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_15::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' at 20:439104 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_2::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_8::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_16::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 PASSED tests/tabix_test.py::TestVCFFromVariantFile_20::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_12::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_10::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' at 20:676148 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_6::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'CallSetAC' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CallSetAC2' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' at 20:669442 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_23::testParsing [W::vcf_parse_info] INFO 'sumGLbyD' is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testConnecting [E::bcf_hdr_parse] Could not parse the header, sample line not found PASSED tests/tabix_test.py::TestVCFFromVariantFile_issue85::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_vcf_v42::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_7::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_5::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_4::testParsing [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_format] FORMAT 'GT' at 20:249843 is not defined in the header, assuming Type=String PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_18::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'AF1' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'CI95' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'DP4' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'MQ' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'PV4' is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PL' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GT' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'GQ' at chr1:1281168 is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2a' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr2b' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr3' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr4' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr5' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_cox_hap1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6_qbl_hap2' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr6' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr7' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr8' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr9' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr10' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr11' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr12' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr13' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr14' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr15' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr16' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse] Contig 'chr17' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testConnecting [E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either the fields are incorrect or spaces are present instead of tabs: #CHROM POS ID REF ALT QUAL FILTER INFO PASSED tests/tabix_test.py::TestVCFFromVariantFile_24::testParsing PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testConnecting PASSED tests/tabix_test.py::TestVCFFromVariantFile_22::testParsing [W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.) [W::vcf_parse_info] INFO 'refseq.name' is not defined in the header, assuming Type=String [W::vcf_parse_info] INFO 'refseq.positionType' is not defined in the header, assuming Type=String [W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testConnecting [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 PASSED tests/tabix_test.py::TestVCFFromVariantFile_21::testParsing [W::bcf_hdr_register_hrec] The definition of Flag "INFO/NotCalledInValidationSamples" is invalid, forcing Number=0 [W::vcf_parse] Contig '20' is not defined in the header. (Quick workaround: index the file with tabix.) PASSED tests/tabix_test.py::TestIndexArgument::testFetchAll PASSED tests/tabix_test.py::TestIndexArgument::testLoadIndexWithoutTbiExtension PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testBED0v26 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testEmpty PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v23 PASSED tests/tabix_test.py::TestBackwardsCompatibility::testVCF0v26 PASSED tests/tabix_test.py::TestMultipleIterators::testDisjointIterators PASSED tests/tabix_test.py::TestMultipleIterators::testDoubleFetch PASSED tests/tabix_test.py::TestMultipleIterators::testJoinedIterators PASSED tests/tabix_test.py::TestMultipleIterators::testScope PASSED tests/tabix_test.py::TestContextManager::testManager PASSED tests/tabix_test.py::TestMultithreadTabixFile::testMultithreadEqualsSinglethread PASSED tests/tabixproxies_test.py::TestBED::testAssignmentToTargetList PASSED tests/tabixproxies_test.py::TestParser::testAssignmentToTargetList PASSED tests/tabixproxies_test.py::TestParser::testCopy PASSED tests/tabixproxies_test.py::TestParser::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestParser::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestParser::testRead PASSED tests/tabixproxies_test.py::TestParser::testUnset PASSED tests/tabixproxies_test.py::TestParser::testWrite PASSED tests/tabixproxies_test.py::TestGTF::testAssignmentToTargetList PASSED tests/tabixproxies_test.py::TestGTF::testCopy PASSED tests/tabixproxies_test.py::TestGTF::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGTF::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGTF::testRead PASSED tests/tabixproxies_test.py::TestGTF::testUnset PASSED tests/tabixproxies_test.py::TestGTF::testWrite PASSED tests/tabixproxies_test.py::TestGTF::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGTF::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGTF::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGTF::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_fields PASSED tests/tabixproxies_test.py::TestGTF::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGTF::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGTF::test_setting_strand_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::testAssignmentToTargetList PASSED tests/tabixproxies_test.py::TestGFF3::testCopy PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorCompressed PASSED tests/tabixproxies_test.py::TestGFF3::testIteratorUncompressed PASSED tests/tabixproxies_test.py::TestGFF3::testRead PASSED tests/tabixproxies_test.py::TestGFF3::testUnset PASSED tests/tabixproxies_test.py::TestGFF3::testWrite PASSED tests/tabixproxies_test.py::TestGFF3::test_added_attribute_is_output PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_can_be_modified PASSED tests/tabixproxies_test.py::TestGFF3::test_asdict_contains_attributes PASSED tests/tabixproxies_test.py::TestGFF3::test_setAttribute_makes_changes PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_end_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_feature_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_fields PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_frame_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_score_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_source_to_none_produces_dot PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_start_is_one_based PASSED tests/tabixproxies_test.py::TestGFF3::test_setting_strand_to_none_produces_dot PASSED tests/test_samtools_python.py::test_idxstats_parse_split_lines PASSED tests/test_samtools_python.py::test_bedcov_split_lines PASSED tests/test_samtools_python.py::test_idxstats_parse PASSED tests/test_samtools_python.py::test_bedcov PASSED =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/pyximport/pyximport.py:51 /usr/lib/python3/dist-packages/pyximport/pyximport.py:51: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses import imp ../../../../../../usr/lib/python3/dist-packages/Cython/Tempita/__init__.py:4 /usr/lib/python3/dist-packages/Cython/Tempita/__init__.py:4: DeprecationWarning: 'cgi' is deprecated and slated for removal in Python 3.13 from ._tempita import * ../../../../../../usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369 /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: /<>/.pybuild/cpython3_3.11_pysam/build/tests/_compile_test.pyx tree = Parsing.p_module(s, pxd, full_module_name) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================= 938 passed, 11 skipped, 3 warnings in 17.17s ================= make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:275: /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/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer, pypa/build or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying pysam/config.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing requirements to pysam.egg-info/requires.txt writing top-level names to pysam.egg-info/top_level.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]' warning: no files found matching 'htslib/LICENSE' warning: no files found matching 'htslib/README' warning: no files found matching '*.[ch]' under directory 'htslib' warning: no previously-included files found matching 'htslib/*config*.h' warning: no files found matching 'htslib/configure.ac' warning: no files found matching 'htslib/m4/*.m4' warning: no files found matching 'htslib/*.in' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/version.sh' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/*.mk' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/libcalignedsegment.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcalignmentfile.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcf.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbcftools.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcbgzf.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcfaidx.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libchtslib.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamfile.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcsamtools.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabix.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libctabixproxies.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcutils.c -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/libcvcf.c -> /<>/.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/cbcftools_util.h -> /<>/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/libctabixproxies.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.pyx -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.pyx -> /<>/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/Pileup.py -> /<>/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/libcbgzf.pyx -> /<>/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/libcfaidx.pyx -> /<>/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.cpython-311-x86_64-linux-gnu.so -> /<>/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/libcsamtools.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.pyx -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.c -> /<>/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/pysam_util.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.pyx -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.c -> /<>/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 creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bin.c.pysam.c -> /<>/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/kmin.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfgtcheck.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfquery.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/HMM.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/em.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfconcat.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/cigar_state.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/version.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam2bcf_iaux.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/mcall.c.pysam.c -> /<>/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/LICENSE -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/dist.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/convert.c -> /<>/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/extsort.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/consensus.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfhead.c -> /<>/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/kheap.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/reheader.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfmerge.c.pysam.c -> /<>/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/bam2bcf_indel.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfnorm.c -> /<>/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/vcmp.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/main.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/cols.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/read_consensus.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/version.sh -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/regidx.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/kmin.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfcall.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfview.c -> /<>/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/vcfplugin.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/ccall.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/prob1.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/str_finder.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/hclust.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfisec.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcffilter.c.pysam.c -> /<>/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/vcfsom.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/dist.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam2bcf_indel.c -> /<>/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/mcall.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /<>/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/rbuf.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.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfroh.c -> /<>/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/vcfconcat.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/extsort.c.pysam.c -> /<>/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/vcfannotate.c -> /<>/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/cols.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/read_consensus.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/ccall.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/mpileup.c -> /<>/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/vcfroh.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/regidx.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcffilter.c -> /<>/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/filter.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfquery.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfbuf.c -> /<>/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/dist.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.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfsort.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/prob1.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/README -> /<>/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/vcfindex.c.pysam.c -> /<>/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/vcfcnv.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/tabix.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/em.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam2bcf.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfstats.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/abuf.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfconvert.c.pysam.c -> /<>/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/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/gvcf.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/mpileup.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/ploidy.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/convert.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/tsv2vcf.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfmerge.c -> /<>/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/vcfcnv.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/ploidy.c.pysam.c -> /<>/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/vcfcall.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/abuf.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfview.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/smpl_ilist.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfplugin.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfstats.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam2bcf.c -> /<>/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/tabix.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfsom.c.pysam.c -> /<>/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/vcfsort.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/csq.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/reheader.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bin.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfnorm.c.pysam.c -> /<>/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/bcftools.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/consensus.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfconvert.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/filter.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/main.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcmp.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/HMM.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/filter.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/extsort.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/version.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam_sample.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/hclust.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/gvcf.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/read_consensus.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfisec.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfbuf.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/csq.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfannotate.c.pysam.c -> /<>/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/vcfhead.c.pysam.c -> /<>/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/mw.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/vcfindex.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_import.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/reset.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_stat.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sam_opts.c -> /<>/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/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/bam_plbuf.c -> /<>/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/LICENSE -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/stats_isize.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_ampliconclip.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_flags.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_color.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_plcmd.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_split.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_lpileup.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_reheader.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bedcov.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_consensus.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_rmdup.c -> /<>/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/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/bam_stat.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_markdup.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/version.sh -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/samtools.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/padding.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_plcmd.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bedidx.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_mate.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sam_opts.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_samples.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bamtk.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/reference.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_fastq.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/reference.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bedidx.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/stats.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_addrprg.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sample.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam2depth.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bamshuf.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_md.c -> /<>/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 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/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/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_sort.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/dict.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_split.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_lpileup.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/amplicon_stats.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sam_utils.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_cat.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bamshuf.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/coverage.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_fastq.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bedcov.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_reheader.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_color.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/consensus_pileup.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_consensus.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_mate.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bamtk.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/reset.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/README -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/amplicon_stats.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/cut_target.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_samples.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/stats_isize.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_quickcheck.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/phase.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_flags.c -> /<>/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/sam_view.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/consensus_pileup.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sam_view.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sam_utils.c -> /<>/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/sample.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_index.c.pysam.c -> /<>/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/tmp_file.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/cram_size.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_rmdupse.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/phase.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_cat.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/sam_utils.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/faidx.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/tmp_file.c -> /<>/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.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/padding.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/dict.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_markdup.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_import.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_md.c.pysam.c -> /<>/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.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_plbuf.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/cram_size.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/stats.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools/lz4 copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/lz4/lz4.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools/lz4 copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/lz4/LICENSE -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools/lz4 copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/lz4/lz4.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools/lz4 copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/lz4/lz4.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools/lz4 copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/cut_target.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_rmdup.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_sort.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/coverage.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_index.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_aux.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam2depth.c.pysam.c -> /<>/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_aux.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/faidx.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/bam_addrprg.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/__init__.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include 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/py.typed -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.c -> /<>/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/version.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.c -> /<>/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/libcbcftools.pxd -> /<>/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/libcutils.pyi -> /<>/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/libcfaidx.c -> /<>/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/libcfaidx.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-x86_64-linux-gnu.so -> /<>/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/libcvcf.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.pyx -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.pyx -> /<>/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/version.pyi -> /<>/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/libctabixproxies.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/__init__.cpython-311.pyc -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/samtools.cpython-311.pyc -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/Pileup.cpython-311.pyc -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/config.cpython-311.pyc -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/utils.cpython-311.pyc -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/version.cpython-311.pyc -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/__pycache__/bcftools.cpython-311.pyc -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__pycache__ copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/htslib_util.c -> /<>/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/libcsamtools.pyi -> /<>/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/libcalignedsegment.pyx -> /<>/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/libcbcftools.cpython-311-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.cpython-311-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.pyx -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.pyx -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-x86_64-linux-gnu.so -> /<>/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/libchtslib.pyx -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-x86_64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.pyx -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.c -> /<>/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/libcbcftools.c -> /<>/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/libcbgzf.pyi -> /<>/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/libcalignmentfile.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/libcbcftools.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_util.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam 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/include/__init__.py to __init__.cpython-311.pyc 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/samtools.py to samtools.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/bcftools.py to bcftools.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/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 running install_egg_info Copying pysam.egg-info to /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam-0.21.0.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 find debian -name LICENSE -delete make[1]: Leaving directory '/<>' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libctabix.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 21a0515825360ee4a0b741207b5e40660bf67842 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libchtslib.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 0c270049d8c6fa642034337e7cbde41d85c80953 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcf.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 c15e588f71de1cafdf2504fe7b9dd85a7e838925 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 2c8d15333c25b9392e6c1e56cbff567fc08075f7 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcutils.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 927bf5c50b4dbc31b4d573be540d2c08b15d977c debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcsamtools.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 89f654fe212cd5766818bc50e352a41e471dc4aa debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcalignedsegment.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 d7de7f63e2c93c76816b332783642c80aa310486 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcftools.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 c4994752a89d4aa2e83eef0b8011fc1b571ef7eb debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcvcf.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 c1ffb24051a3806c2b282e3d2d7f73c19ddf8632 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbgzf.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 92e5d8ec2b446e3766a5df5b55e8b07792d188ee debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 6007985ccae5eeb2b2ce19e166ae98d102a0ae89 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 55de6c0b7b73659d520771fa4530d4d5150c1358 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcalignmentfile.cpython-311-x86_64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 a3c7ea6a008720ab120d20b0ff1823b65a880c2a dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 153 INFO: pkgstriptranslations version 153 INFO: pkgstriptranslations version 153 pkgstriptranslations: processing python3-pysam (in debian/python3-pysam); do_strip: , oemstrip: pkgstriptranslations: processing python-pysam-tests (in debian/python-pysam-tests); 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 " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-pysam/DEBIAN/control, package python3-pysam, directory debian/python3-pysam pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-pysam ... pkgstripfiles: processing control file: debian/python-pysam-tests/DEBIAN/control, package python-pysam-tests, directory debian/python-pysam-tests pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.21.0+ds-1_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package python-pysam-tests ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python-pysam-tests' in '../python-pysam-tests_0.21.0+ds-1_all.deb'. 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_0.21.0+ds-1_amd64.deb'. Renaming python3-pysam-dbgsym_0.21.0+ds-1_amd64.deb to python3-pysam-dbgsym_0.21.0+ds-1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../python-pysam_0.21.0+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../python-pysam_0.21.0+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-06-24T11:28:52Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pysam_0.21.0+ds-1_amd64.changes: --------------------------------------- Format: 1.8 Date: Fri, 23 Jun 2023 20:10:54 +0200 Source: python-pysam Binary: python-pysam-tests python3-pysam Built-For-Profiles: noudeb Architecture: all amd64 Version: 0.21.0+ds-1 Distribution: mantic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping format ( python3-pysam - interface for the SAM/BAM sequence alignment and mapping format ( Changes: python-pysam (0.21.0+ds-1) unstable; urgency=medium . * New upstream version * Patches triage: - disable-tests-python3.11.patch removed: applied upstream - python3.11.patch removed: applied upstream - skip_test_remote.patch: forwarding not-needed - skip-test-on-32-bit.patch: provide dep3 header - clean_less patch: forwarding not-needed * d/copyright: bump copyright year. * d/rules: delete extra license files. * typos.patch: add; fix typos caught by lintian. 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libpython3.11-minimal (= 3.11.4-1), libpython3.11-stdlib (= 3.11.4-1), libquadmath0 (= 13.1.0-6ubuntu1), libreadline8 (= 8.2-1.3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-1), libsasl2-modules-db (= 2.1.28+dfsg1-1), libseccomp2 (= 2.5.4-1ubuntu3), libselinux1 (= 3.4-1build4), libsmartcols1 (= 2.38.1-5ubuntu2), libsqlite3-0 (= 3.40.1-2), libssh-4 (= 0.10.5-2), libssl3 (= 3.0.9-1ubuntu1), libstdc++-12-dev (= 12.3.0-3ubuntu1), libstdc++6 (= 13.1.0-6ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.5-2ubuntu3), libtasn1-6 (= 4.19.0-2), libtinfo6 (= 6.4-4), 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), libtsan2 (= 13.1.0-6ubuntu1), libubsan1 (= 13.1.0-6ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 252.5-2ubuntu3), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-5ubuntu2), libxml2 (= 2.9.14+dfsg-1.2), libzstd1 (= 1.5.4+dfsg2-5), linux-libc-dev (= 6.3.0-7.7), login (= 1:4.13+dfsg1-1ubuntu1), lto-disabled-list (= 41), m4 (= 1.4.19-3), make (= 4.3-4.1build1), man-db (= 2.11.2-2), mawk (= 1.3.4.20230525-1), media-types (= 10.0.0), ncurses-base (= 6.4-4), ncurses-bin (= 6.4-4), patch (= 2.7.6-7build2), perl (= 5.36.0-7ubuntu1), perl-base (= 5.36.0-7ubuntu1), perl-modules-5.36 (= 5.36.0-7ubuntu1), 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 (= 3.11.4-1), python3-iniconfig (= 1.1.1-2), python3-lib2to3 (= 3.11.4-1), python3-minimal (= 3.11.2-1), python3-more-itertools (= 9.1.1-2), python3-packaging (= 23.1-1), python3-pkg-resources (= 67.8.0-1), python3-pluggy (= 1.0.0+repack-1), python3-py (= 1.11.0-1), python3-pytest (= 7.3.2-1), python3-setuptools (= 67.8.0-1), python3.11 (= 3.11.4-1), python3.11-dev (= 3.11.4-1), python3.11-minimal (= 3.11.4-1), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.2-0ubuntu6), samtools (= 1.17-1), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.06-4ubuntu1), tabix (= 1.17+ds-1), tar (= 1.34+dfsg-1.2ubuntu1), usrmerge (= 35ubuntu1), util-linux (= 2.38.1-5ubuntu2), util-linux-extra (= 2.38.1-5ubuntu2), 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="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1687543854" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python-pysam-tests_0.21.0+ds-1_all.deb -------------------------------------- new Debian package, version 2.0. size 1429520 bytes: control archive=4881 bytes. 738 bytes, 19 lines control 16851 bytes, 179 lines md5sums Package: python-pysam-tests Source: python-pysam Version: 0.21.0+ds-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2774 Enhances: python3-pysam Section: python Priority: optional Multi-Arch: foreign Homepage: https://pysam.readthedocs.org/en/latest Description: interface for the SAM/BAM sequence alignment and mapping format (test data) 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 contains the data provided by upstream to run the pysam test suite. drwxr-xr-x root/root 0 2023-06-23 18:10 ./ drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/ drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/share/ drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/share/doc/python-pysam-tests/ -rw-r--r-- root/root 306 2023-06-23 18:10 ./usr/share/doc/python-pysam-tests/README.Debian -rw-r--r-- root/root 2200 2023-06-23 18:10 ./usr/share/doc/python-pysam-tests/changelog.Debian.gz -rw-r--r-- root/root 2687 2023-06-23 18:10 ./usr/share/doc/python-pysam-tests/copyright drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/share/doc/python-pysam/ drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/share/doc/python-pysam/tests/ -rw-r--r-- root/root 678 2023-04-01 21:14 ./usr/share/doc/python-pysam/tests/00README.txt -rw-r--r-- root/root 677 2023-04-01 21:14 ./usr/share/doc/python-pysam/tests/AlignedSegment_bench.py -rw-r--r-- root/root 9825 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./usr/share/doc/python-pysam/tests/test_samtools_python.py drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/share/lintian/ drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 247 2023-06-23 18:10 ./usr/share/lintian/overrides/python-pysam-tests python3-pysam_0.21.0+ds-1_amd64.deb ----------------------------------- new Debian package, version 2.0. size 3143434 bytes: control archive=9134 bytes. 782 bytes, 17 lines control 34503 bytes, 352 lines md5sums 273 bytes, 12 lines * postinst #!/bin/sh 386 bytes, 12 lines * prerm #!/bin/sh Package: python3-pysam Source: python-pysam Version: 0.21.0+ds-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 28227 Depends: libc6 (>= 2.34), libhts3 (>= 1.17), zlib1g (>= 1:1.1.4), cython3, 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. . 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+------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 211188 Build-Time: 193 Distribution: mantic-proposed Host Architecture: amd64 Install-Time: 12 Job: python-pysam_0.21.0+ds-1.dsc Machine Architecture: amd64 Package: python-pysam Package-Time: 205 Source-Version: 0.21.0+ds-1 Space: 211188 Status: successful Version: 0.21.0+ds-1 -------------------------------------------------------------------------------- Finished at 2023-06-24T11:28:52Z Build needed 00:03:25, 211188k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26335195 Scanning for processes to kill in build PACKAGEBUILD-26335195