https://launchpad.net/ubuntu/+source/python-pysam/0.21.0+ds-1/+build/26335199 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lgw01-030 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 Buildd toolchain package versions: launchpad-buildd_233~634~ubuntu20.04.1 python3-lpbuildd_233~634~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 24 Jun 11:22:47 ntpdate[3552864]: adjust time server 10.211.37.1 offset -0.000441 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26335199 --image-type chroot /home/buildd/filecache-default/859743d4aa431be74cb50b11ddbd51d0d1ab094f Creating target for build PACKAGEBUILD-26335199 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26335199 Starting target for build PACKAGEBUILD-26335199 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26335199 '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-26335199 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26335199 Updating target for build PACKAGEBUILD-26335199 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 riscv64 Packages [1320 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe riscv64 Packages [13.9 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5936 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 Packages [51.6 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [24.2 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 Packages [455 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [169 kB] Fetched 22.9 MB in 43s (538 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-riscv64-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 libgssapi-krb5-2 libisl23 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblzma5 libmd0 libmount1 libmpfr6 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 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 132 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 93.3 MB of archives. After this operation, 2836 kB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcrypt-dev riscv64 1:4.4.35-1 [235 kB] Get:2 http://ftpmaster.internal/ubuntu mantic/main riscv64 libc6-dev riscv64 2.37-0ubuntu2 [3134 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main riscv64 libc-dev-bin riscv64 2.37-0ubuntu2 [18.8 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcrypt1 riscv64 1:4.4.35-1 [94.6 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main riscv64 linux-libc-dev riscv64 6.3.0-7.7 [1512 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main riscv64 libc6 riscv64 2.37-0ubuntu2 [2609 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main riscv64 libc-bin riscv64 2.37-0ubuntu2 [551 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main riscv64 gcc-13-base riscv64 13.1.0-6ubuntu1 [42.0 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgcc-s1 riscv64 13.1.0-6ubuntu1 [57.2 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main riscv64 base-files riscv64 13ubuntu1 [73.7 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main riscv64 bash riscv64 5.2.15-2ubuntu1 [672 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main riscv64 bsdutils riscv64 1:2.38.1-5ubuntu2 [101 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main riscv64 coreutils riscv64 9.1-1ubuntu2 [1309 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main riscv64 liblzma5 riscv64 5.4.1-0.2 [115 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgcrypt20 riscv64 1.10.1-3ubuntu1 [503 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main riscv64 libstdc++6 riscv64 13.1.0-6ubuntu1 [779 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main riscv64 libacl1 riscv64 2.3.1-3 [15.7 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main riscv64 libapparmor1 riscv64 3.0.8-1ubuntu3 [43.1 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main riscv64 libaudit-common all 1:3.0.9-1 [5142 B] Get:20 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcap-ng0 riscv64 0.8.3-1build2 [13.6 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main riscv64 libaudit1 riscv64 1:3.0.9-1 [44.0 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main riscv64 libblkid1 riscv64 2.38.1-5ubuntu2 [155 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcap2 riscv64 1:2.66-4ubuntu1 [26.5 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main riscv64 libperl5.36 riscv64 5.36.0-7ubuntu1 [4203 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main riscv64 perl riscv64 5.36.0-7ubuntu1 [235 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main riscv64 perl-base riscv64 5.36.0-7ubuntu1 [1655 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main riscv64 perl-modules-5.36 all 5.36.0-7ubuntu1 [2984 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdb5.3 riscv64 5.3.28+dfsg2-1 [691 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main riscv64 zlib1g riscv64 1:1.2.13.dfsg-1ubuntu4 [54.0 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main riscv64 debconf all 1.5.82 [125 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main riscv64 libssl3 riscv64 3.0.9-1ubuntu1 [1453 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main riscv64 libzstd1 riscv64 1.5.4+dfsg2-5 [310 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main riscv64 libkmod2 riscv64 30+20221128-1ubuntu1 [43.5 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpcre2-8-0 riscv64 10.42-1 [142 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main riscv64 libselinux1 riscv64 3.4-1build4 [71.6 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main riscv64 libmount1 riscv64 2.38.1-5ubuntu2 [155 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpam0g riscv64 1.5.2-6ubuntu1 [61.6 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main riscv64 libseccomp2 riscv64 2.5.4-1ubuntu3 [47.0 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main riscv64 systemd-sysv riscv64 252.5-2ubuntu3 [11.5 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main riscv64 systemd riscv64 252.5-2ubuntu3 [2815 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsystemd-shared riscv64 252.5-2ubuntu3 [1629 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main riscv64 libatomic1 riscv64 13.1.0-6ubuntu1 [9548 B] Get:43 http://ftpmaster.internal/ubuntu mantic/main riscv64 libargon2-1 riscv64 0~20190702+dfsg-3 [19.9 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main riscv64 libudev1 riscv64 252.5-2ubuntu3 [143 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdevmapper1.02.1 riscv64 2:1.02.185-2ubuntu1 [131 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main riscv64 libuuid1 riscv64 2.38.1-5ubuntu2 [33.2 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcryptsetup12 riscv64 2:2.6.1-4ubuntu1 [210 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfdisk1 riscv64 2.38.1-5ubuntu2 [194 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main riscv64 libp11-kit0 riscv64 0.24.1-2ubuntu1 [196 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main riscv64 mount riscv64 2.38.1-5ubuntu2 [129 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsystemd0 riscv64 252.5-2ubuntu3 [360 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main riscv64 libapt-pkg6.0 riscv64 2.7.1 [935 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main riscv64 tar riscv64 1.34+dfsg-1.2ubuntu1 [271 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main riscv64 dpkg riscv64 1.21.22ubuntu1 [1352 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main riscv64 dash riscv64 0.5.12-2ubuntu1 [81.8 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main riscv64 diffutils riscv64 1:3.8-4 [167 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main riscv64 findutils riscv64 4.9.0-4ubuntu1 [295 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main riscv64 grep riscv64 3.8-5 [155 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main riscv64 hostname riscv64 3.23+nmu1ubuntu1 [10.5 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main riscv64 ncurses-bin riscv64 6.4-4 [177 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main riscv64 sed riscv64 4.9-1 [191 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsmartcols1 riscv64 2.38.1-5ubuntu2 [109 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main riscv64 util-linux-extra riscv64 2.38.1-5ubuntu2 [104 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main riscv64 util-linux riscv64 2.38.1-5ubuntu2 [1150 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main riscv64 ncurses-base all 6.4-4 [23.3 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main riscv64 sysvinit-utils riscv64 3.06-4ubuntu1 [32.9 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/main riscv64 lsb-base all 11.6 [4606 B] Get:68 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 adduser all 3.134ubuntu1 [136 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main riscv64 gpgv riscv64 2.2.40-1.1ubuntu1 [205 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgnutls30 riscv64 3.7.9-2ubuntu1 [907 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main riscv64 apt riscv64 2.7.1 [1308 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpam-modules-bin riscv64 1.5.2-6ubuntu1 [44.8 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpam-modules riscv64 1.5.2-6ubuntu1 [267 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main riscv64 logsave riscv64 1.47.0-1ubuntu1 [13.7 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main riscv64 libext2fs2 riscv64 1.47.0-1ubuntu1 [197 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main riscv64 e2fsprogs riscv64 1.47.0-1ubuntu1 [555 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main riscv64 libattr1 riscv64 1:2.5.1-4 [11.4 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdebconfclient0 riscv64 0.267ubuntu1 [7418 B] Get:79 http://ftpmaster.internal/ubuntu mantic/main riscv64 libmd0 riscv64 1.1.0-1 [28.3 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB] Get:81 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsemanage-common all 3.4-1build4 [9852 B] Get:82 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsepol2 riscv64 3.4-2.1 [258 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsemanage2 riscv64 3.4-1build4 [83.5 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main riscv64 libncurses6 riscv64 6.4-4 [93.2 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main riscv64 libncursesw6 riscv64 6.4-4 [126 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main riscv64 libtinfo6 riscv64 6.4-4 [92.6 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main riscv64 usrmerge all 35ubuntu1 [58.2 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcom-err2 riscv64 1.47.0-1ubuntu1 [13.5 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main riscv64 libproc2-0 riscv64 2:4.0.3-1ubuntu1 [45.2 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main riscv64 libss2 riscv64 1.47.0-1ubuntu1 [15.2 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/main riscv64 mawk riscv64 1.3.4.20230525-1 [103 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main riscv64 procps riscv64 2:4.0.3-1ubuntu1 [598 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main riscv64 sensible-utils all 0.0.20 [19.6 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main riscv64 openssl riscv64 3.0.9-1ubuntu1 [1149 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main riscv64 ca-certificates all 20230311ubuntu1 [152 kB] Get:96 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgssapi-krb5-2 riscv64 1.20.1-2 [125 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main riscv64 libkrb5-3 riscv64 1.20.1-2 [329 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main riscv64 libkrb5support0 riscv64 1.20.1-2 [31.3 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main riscv64 libk5crypto3 riscv64 1.20.1-2 [96.5 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main riscv64 readline-common all 8.2-1.3 [55.7 kB] Get:101 http://ftpmaster.internal/ubuntu mantic/main riscv64 libreadline8 riscv64 8.2-1.3 [131 kB] Get:102 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsqlite3-0 riscv64 3.40.1-2 [586 kB] Get:103 http://ftpmaster.internal/ubuntu mantic/main riscv64 tzdata all 2023c-4exp1ubuntu1 [271 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main riscv64 xz-utils riscv64 5.4.1-0.2 [266 kB] Get:105 http://ftpmaster.internal/ubuntu mantic/main riscv64 advancecomp riscv64 2.5-1 [216 kB] Get:106 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libctf0 riscv64 2.40.50.20230622-1ubuntu1 [87.5 kB] Get:107 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libctf-nobfd0 riscv64 2.40.50.20230622-1ubuntu1 [89.0 kB] Get:108 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 binutils-riscv64-linux-gnu riscv64 2.40.50.20230622-1ubuntu1 [827 kB] Get:109 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libbinutils riscv64 2.40.50.20230622-1ubuntu1 [460 kB] Get:110 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 binutils riscv64 2.40.50.20230622-1ubuntu1 [2992 B] Get:111 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 binutils-common riscv64 2.40.50.20230622-1ubuntu1 [219 kB] Get:112 http://ftpmaster.internal/ubuntu mantic/main riscv64 libisl23 riscv64 0.26-3 [604 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main riscv64 libmpfr6 riscv64 4.2.0-1 [260 kB] Get:114 http://ftpmaster.internal/ubuntu mantic/main riscv64 g++-12 riscv64 12.3.0-3ubuntu1 [9551 kB] Get:115 http://ftpmaster.internal/ubuntu mantic/main riscv64 gcc-12 riscv64 12.3.0-3ubuntu1 [16.3 MB] Get:116 http://ftpmaster.internal/ubuntu mantic/main riscv64 cpp-12 riscv64 12.3.0-3ubuntu1 [8279 kB] Get:117 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgomp1 riscv64 13.1.0-6ubuntu1 [140 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/main riscv64 libasan8 riscv64 13.1.0-6ubuntu1 [2500 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main riscv64 libstdc++-12-dev riscv64 12.3.0-3ubuntu1 [4916 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/main riscv64 libgcc-12-dev riscv64 12.3.0-3ubuntu1 [2637 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcc1-0 riscv64 13.1.0-6ubuntu1 [45.4 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/main riscv64 gcc-12-base riscv64 12.3.0-3ubuntu1 [42.8 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/main riscv64 g++ riscv64 4:12.2.0-3ubuntu1 [1108 B] Get:124 http://ftpmaster.internal/ubuntu mantic/main riscv64 gcc riscv64 4:12.2.0-3ubuntu1 [5178 B] Get:125 http://ftpmaster.internal/ubuntu mantic/main riscv64 cpp riscv64 4:12.2.0-3ubuntu1 [27.8 kB] Get:126 http://ftpmaster.internal/ubuntu mantic/main riscv64 dpkg-dev all 1.21.22ubuntu1 [1118 kB] Get:127 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdpkg-perl all 1.21.22ubuntu1 [247 kB] Get:128 http://ftpmaster.internal/ubuntu mantic/main riscv64 lto-disabled-list all 41 [12.4 kB] Get:129 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfakeroot riscv64 1.31-1.2 [27.6 kB] Get:130 http://ftpmaster.internal/ubuntu mantic/main riscv64 fakeroot riscv64 1.31-1.2 [67.9 kB] Get:131 http://ftpmaster.internal/ubuntu mantic/main riscv64 gpg riscv64 2.2.40-1.1ubuntu1 [491 kB] Get:132 http://ftpmaster.internal/ubuntu mantic/main riscv64 gpgconf riscv64 2.2.40-1.1ubuntu1 [121 kB] Get:133 http://ftpmaster.internal/ubuntu mantic/main riscv64 gpg-agent riscv64 2.2.40-1.1ubuntu1 [239 kB] Get:134 http://ftpmaster.internal/ubuntu mantic/main riscv64 pkgbinarymangler all 153 [16.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 93.3 MB in 24s (3960 kB/s) (Reading database ... 13011 files and directories currently installed.) 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Setting up libdpkg-perl (1.21.22ubuntu1) ... Setting up cpp (4:12.2.0-3ubuntu1) ... Setting up gpgconf (2.2.40-1.1ubuntu1) ... Setting up libc6-dev:riscv64 (2.37-0ubuntu2) ... Setting up gpg (2.2.40-1.1ubuntu1) ... Setting up gpg-agent (2.2.40-1.1ubuntu1) ... Setting up libstdc++-12-dev:riscv64 (12.3.0-3ubuntu1) ... Setting up systemd (252.5-2ubuntu3) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up dpkg-dev (1.21.22ubuntu1) ... Setting up gcc-12 (12.3.0-3ubuntu1) ... Setting up g++-12 (12.3.0-3ubuntu1) ... Setting up systemd-sysv (252.5-2ubuntu3) ... Setting up gcc (4:12.2.0-3ubuntu1) ... Setting up g++ (4:12.2.0-3ubuntu1) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... Processing triggers for debianutils (5.7-0.4) ... Processing triggers for ca-certificates (20230311ubuntu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-26335199 riscv64 mantic-proposed -c chroot:build-PACKAGEBUILD-26335199 --arch=riscv64 --dist=mantic-proposed --nolog python-pysam_0.21.0+ds-1.dsc Initiating build PACKAGEBUILD-26335199 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lgw01-030.buildd +==============================================================================+ | python-pysam 0.21.0+ds-1 (riscv64) Sat, 24 Jun 2023 11:34:21 +0000 | +==============================================================================+ Package: python-pysam Version: 0.21.0+ds-1 Source Version: 0.21.0+ds-1 Distribution: mantic-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26335199/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-K4p9Fx/resolver-RbkmN2' 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-K4p9Fx/python-pysam-0.21.0+ds' with '<>' I: NOTICE: Log filtering will replace 'build/python-pysam-K4p9Fx' 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 [529 B] Fetched 1941 B in 1s (3281 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bcftools bsdextrautils cython3 debhelper debugedit dh-autoreconf dh-exec dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72 libjs-jquery libjs-sphinxdoc libjs-underscore libldap2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3 python3-all python3-all-dev python3-attr python3-dev python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-more-itertools python3-packaging python3-pkg-resources python3-pluggy python3-py python3-pytest python3-setuptools python3.11 python3.11-dev python3.11-minimal samtools tabix zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc python3-numpy python3-matplotlib texlive-latex-recommended cython-doc dh-make flit python3-build python3-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. Need to get 52.7 MB of archives. After this operation, 268 MB of additional disk space will be used. 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mantic/main riscv64 libbrotli1 riscv64 1.0.9-2build8 [324 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsasl2-modules-db riscv64 2.1.28+dfsg1-1 [19.2 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsasl2-2 riscv64 2.1.28+dfsg1-1 [54.0 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main riscv64 libldap2 riscv64 2.6.3+dfsg-1~exp1ubuntu2 [163 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2build4 [54.6 kB] Get:36 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 libssh-4 riscv64 0.10.5-2 [163 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcurl3-gnutls riscv64 7.88.1-10ubuntu1 [265 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdeflate0 riscv64 1.15-1 [36.8 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/universe riscv64 libhtscodecs2 riscv64 1.5.0-1 [80.7 kB] Get:40 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 libhts3 riscv64 1.17+ds-1 [390 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/universe riscv64 bcftools riscv64 1.16-1 [680 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/universe riscv64 cython3 riscv64 0.29.32-2ubuntu2 [1256 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdebhelper-perl all 13.11.4ubuntu3 [66.1 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main riscv64 libtool all 2.4.7-5 [166 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main riscv64 dh-autoreconf all 20 [16.1 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main riscv64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main riscv64 libsub-override-perl all 0.09-4 [8706 B] Get:48 http://ftpmaster.internal/ubuntu mantic/main riscv64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main riscv64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:50 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdw1 riscv64 0.188-2.1 [229 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main riscv64 debugedit riscv64 1:5.0-5 [48.8 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main riscv64 dwz riscv64 0.15-1 [115 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main riscv64 gettext riscv64 0.21-12 [811 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main riscv64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main riscv64 po-debconf all 1.0.21+nmu1 [233 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main riscv64 debhelper all 13.11.4ubuntu3 [925 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-lib2to3 all 3.11.4-1 [79.0 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-distutils all 3.11.4-1 [131 kB] Get:59 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 dh-python all 6.20230603 [107 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main riscv64 libcurl4-gnutls-dev riscv64 7.88.1-10ubuntu1 [874 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main riscv64 libdeflate-dev riscv64 1.15-1 [83.7 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main riscv64 libexpat1-dev riscv64 2.5.0-2 [292 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main riscv64 liblzma-dev riscv64 5.4.1-0.2 [314 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main riscv64 zlib1g-dev riscv64 1:1.2.13.dfsg-1ubuntu4 [957 kB] Get:65 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 libhts-dev riscv64 1.17+ds-1 [3659 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main riscv64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/main riscv64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main riscv64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpython3.11 riscv64 3.11.4-1 [1932 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpython3.11-dev riscv64 3.11.4-1 [13.8 MB] Get:71 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpython3-dev riscv64 3.11.2-1 [7492 B] Get:72 http://ftpmaster.internal/ubuntu mantic/main riscv64 libpython3-all-dev riscv64 3.11.2-1 [908 B] Get:73 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-all riscv64 3.11.2-1 [898 B] Get:74 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3.11-dev riscv64 3.11.4-1 [500 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-dev riscv64 3.11.2-1 [26.8 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-all-dev riscv64 3.11.2-1 [906 B] Get:77 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-attr all 22.2.0-1 [49.6 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-iniconfig all 1.1.1-2 [6024 B] Get:79 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3-more-itertools all 9.1.1-2 [51.3 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main riscv64 python3-packaging all 23.1-1 [38.1 kB] Get:81 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-pluggy all 1.0.0+repack-1 [15.1 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/universe riscv64 python3-py all 1.11.0-1 [73.2 kB] Get:83 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 python3-pytest all 7.3.2-1 [241 kB] Get:84 http://ftpmaster.internal/ubuntu mantic-proposed/main riscv64 python3-setuptools all 67.8.0-1 [392 kB] Get:85 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 samtools riscv64 1.17-1 [600 kB] Get:86 http://ftpmaster.internal/ubuntu mantic-proposed/universe riscv64 tabix riscv64 1.17+ds-1 [431 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main riscv64 dh-exec riscv64 0.27 [24.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 52.7 MB in 14s (3851 kB/s) Selecting previously unselected package libpython3.11-minimal:riscv64. (Reading database ... 12511 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.4-1_riscv64.deb ... Unpacking libpython3.11-minimal:riscv64 (3.11.4-1) ... Selecting previously unselected package libexpat1:riscv64. Preparing to unpack .../libexpat1_2.5.0-2_riscv64.deb ... Unpacking libexpat1:riscv64 (2.5.0-2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.4-1_riscv64.deb ... Unpacking python3.11-minimal (3.11.4-1) ... Setting up libpython3.11-minimal:riscv64 (3.11.4-1) ... Setting up libexpat1:riscv64 (2.5.0-2) ... Setting up python3.11-minimal (3.11.4-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 12825 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.2-1_riscv64.deb ... Unpacking python3-minimal (3.11.2-1) ... Selecting previously unselected package media-types. 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Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11 (3.11.4-1) ... Setting up libdw1:riscv64 (0.188-2.1) ... Setting up gettext (0.21-12) ... Setting up libpython3.11:riscv64 (3.11.4-1) ... Setting up libtool (2.4.7-5) ... Setting up libcurl3-gnutls:riscv64 (7.88.1-10ubuntu1) ... Setting up python3 (3.11.2-1) ... Setting up libcurl4-gnutls-dev:riscv64 (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:riscv64 (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:riscv64 (1.17+ds-1) ... Setting up libpython3-dev:riscv64 (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:riscv64 (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:riscv64 (3.11.2-1) ... Setting up python3-dev (3.11.2-1) ... Setting up python3-all-dev (3.11.2-1) ... Setting up debhelper (13.11.4ubuntu3) ... Setting up dh-exec (0.27) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (252.5-2ubuntu3) ... Processing triggers for libc-bin (2.37-0ubuntu2) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 (riscv64) Toolchain package versions: binutils_2.40.50.20230622-1ubuntu1 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-riscv64-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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libkmod2_30+20221128-1ubuntu1 libkrb5-3_1.20.1-2 libkrb5support0_1.20.1-2 libldap2_2.6.3+dfsg-1~exp1ubuntu2 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblz4-1_1.9.4-1 liblzma-dev_5.4.1-0.2 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.1.0-1 libmount1_2.38.1-5ubuntu2 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libncurses6_6.4-4 libncursesw6_6.4-4 libnettle8_3.8.1-2 libnghttp2-14_1.54.0-1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libp11-kit0_0.24.1-2ubuntu1 libpam-modules_1.5.2-6ubuntu1 libpam-modules-bin_1.5.2-6ubuntu1 libpam-runtime_1.5.2-6ubuntu1 libpam0g_1.5.2-6ubuntu1 libpcre2-8-0_10.42-1 libperl5.36_5.36.0-7ubuntu1 libpipeline1_1.5.7-1 libpng16-16_1.6.39-2 libproc2-0_2:4.0.3-1ubuntu1 libprocps8_2:3.3.17-7ubuntu1 libpsl5_0.21.2-1 libpython3-all-dev_3.11.2-1 libpython3-dev_3.11.2-1 libpython3-stdlib_3.11.2-1 libpython3.11_3.11.4-1 libpython3.11-dev_3.11.4-1 libpython3.11-minimal_3.11.4-1 libpython3.11-stdlib_3.11.4-1 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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=8 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-26335199 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26335199 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26335199 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 riscv64 debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/<>/tests/pysam_data' rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz make[1]: Leaving directory '/<>/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/<>/tests/cbcf_data' rm -f all.stamp *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/<>/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean I: pybuild base: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-riscv64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base: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 -a -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/version.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/__init__.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/Pileup.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/samtools.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/config.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/utils.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam copying pysam/bcftools.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam creating /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include copying pysam/include/__init__.py -> /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include 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-riscv64-cpython-311 creating build/temp.linux-riscv64-cpython-311/pysam riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/htslib_util.o build/temp.linux-riscv64-cpython-311/pysam/libchtslib.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.linux-riscv64-cpython-311/samtools creating build/temp.linux-riscv64-cpython-311/samtools/lz4 riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcsamtools.o build/temp.linux-riscv64-cpython-311/samtools/amplicon_stats.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam2depth.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_addrprg.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_aux.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_cat.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_color.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_consensus.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_fastq.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_flags.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_import.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_index.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_lpileup.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_markdup.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_mate.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_md.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_plbuf.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_plcmd.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_quickcheck.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_reheader.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_rmdup.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_rmdupse.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_samples.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_sort.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_split.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bam_stat.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bamshuf.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bamtk.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bedcov.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/bedidx.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/consensus_pileup.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/coverage.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/cram_size.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/cut_target.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/dict.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/faidx.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/lz4/lz4.o build/temp.linux-riscv64-cpython-311/samtools/padding.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/phase.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/reference.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/reset.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/sam_opts.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/sam_utils.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/sam_view.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/sample.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/samtools.pysam.o build/temp.linux-riscv64-cpython-311/samtools/stats.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/stats_isize.c.pysam.o build/temp.linux-riscv64-cpython-311/samtools/tmp_file.c.pysam.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-riscv64-cpython-311/bcftools riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:751:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 751 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/htslib/kstring.h:30, from /usr/include/htslib/hts.h:37, from /usr/include/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:556:14: note: in a call to allocation function ‘calloc’ declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/bcftools/HMM.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/abuf.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/bam2bcf.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/bam_sample.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/bcftools.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/bin.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/ccall.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/cols.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/consensus.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/convert.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/csq.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/dist.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/em.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/extsort.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/filter.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/gvcf.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/hclust.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/kmin.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/main.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/mcall.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/mpileup.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/ploidy.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/prob1.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/read_consensus.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/regidx.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/reheader.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/smpl_ilist.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/str_finder.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/tabix.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/tsv2vcf.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfannotate.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfbuf.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfcall.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfcnv.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfconcat.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfconvert.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcffilter.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfhead.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfindex.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfisec.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfmerge.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfnorm.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfplugin.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfquery.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfroh.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfsom.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfsort.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfstats.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcfview.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/vcmp.c.pysam.o build/temp.linux-riscv64-cpython-311/bcftools/version.c.pysam.o build/temp.linux-riscv64-cpython-311/pysam/libcbcftools.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcutils.o build/temp.linux-riscv64-cpython-311/pysam/pysam_util.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcsamtools.cpython-311-riscv64-linux-gnu -lcbcftools.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c: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)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcalignmentfile.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-riscv64-cpython-311/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcsamfile.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c: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)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcalignedsegment.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libctabix.c -o build/temp.linux-riscv64-cpython-311/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libctabix.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcfaidx.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: pysam/libcbcf.c: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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcbcf.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcbgzf.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/<>/pysam -I/usr/include -I/<>/samtools -I/<>/samtools/lz4 -I/<>/bcftools -I/<> -I/usr/include/python3.11 -c pysam/libctabixproxies.c -o build/temp.linux-riscv64-cpython-311/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libctabixproxies.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension riscv64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+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-riscv64-cpython-311/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.constprop’: pysam/libcvcf.c: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; | ^~~~~~~~~~~~ riscv64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/python-pysam-0.21.0+ds-1 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-cpython-311/pysam/libcvcf.o -L/<>/pysam -L/usr/lib/riscv64-linux-gnu -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/<>/.pybuild/cpython3_3.11_pysam/build/pysam -L/usr/lib/riscv64-linux-gnu -lz -lhts -lchtslib.cpython-311-riscv64-linux-gnu -lcutils.cpython-311-riscv64-linux-gnu -o /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.cpython-311-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base: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/htslib_util.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/version.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/__init__.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.pyx -> /<>/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/libcvcf.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/libcvcf.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.pyx -> /<>/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/libchtslib.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/libcutils.pyi -> /<>/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/libcbgzf.pyx -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/Pileup.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/py.typed -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.pyx -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_stream.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/samtools.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/config.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_util.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabixproxies.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.pyx -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignmentfile.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.c -> /<>/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/libcbcftools.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/utils.py -> /<>/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/version.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcvcf.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/cbcftools_util.h -> /<>/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/libcalignmentfile.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/pysam_util.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/csamtools_util.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/htslib_util.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.pyx -> /<>/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/libcsamfile.pyi -> /<>/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/libcbcftools.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/__init__.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include creating /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/samtools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/samtools/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/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/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/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/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/samtools.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/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/phase.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_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_lpileup.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/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_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/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/bedidx.h -> /<>/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/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/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_color.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/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/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/bam_aux.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 -> /<>/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/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.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/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/dict.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.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/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/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_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/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_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/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/stats.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/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_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/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/bamtk.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/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/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.h -> /<>/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/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/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/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/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/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/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/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/coverage.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_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/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/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/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/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/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/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/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/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_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/bam.c -> /<>/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/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/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_reheader.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.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_plbuf.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_lpileup.h -> /<>/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/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/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.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/samtools/README -> /<>/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_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_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_md.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_cat.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/reset.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/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_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/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/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/bam2depth.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/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/padding.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.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_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/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/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/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/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/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/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/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_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/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/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/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/sample.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_sort.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 creating /<>/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/dist.h -> /<>/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/vcfcall.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/vcfgtcheck.c -> /<>/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/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/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/filter.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/regidx.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/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/variantkey.h -> /<>/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/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/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/tabix.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 -> /<>/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/vcfisec.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/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/vcfbuf.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/convert.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/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/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/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/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/bam2bcf.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.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_indel.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/ploidy.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/filter.h -> /<>/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/kheap.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/extsort.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/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/kmin.h -> /<>/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/mcall.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/consensus.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/bam2bcf.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.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/utlist.h -> /<>/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.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.pysam.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 -> /<>/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/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/main.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.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.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/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/vcfconcat.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/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/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/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/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/bcftools.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.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/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/tsv2vcf.h -> /<>/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/prob1.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 -> /<>/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 -> /<>/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/vcfconvert.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/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/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/convert.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/vcfbuf.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/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/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/vcfannotate.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.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.h -> /<>/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/vcfview.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/rbuf.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/regidx.h -> /<>/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/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/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/vcfroh.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/hclust.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/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/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/vcfsort.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/abuf.c -> /<>/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/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/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/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/vcfhead.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/csq.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/abuf.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/cols.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/mw.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/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/kmin.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/vcfindex.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/khash_str2str.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/bam_sample.h -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/include/bcftools/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/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/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/vcfplugin.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/vcfmerge.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/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/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/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/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/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/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/HMM.h -> /<>/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/tsv2vcf.c.pysam.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/bcftools copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcalignedsegment.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcfaidx.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcftools.pxd -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.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/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/libctabix.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbcf.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamtools.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcutils.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.pyi -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcbgzf.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libchtslib.c -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/bcftools.py -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libcsamfile.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam copying /<>/.pybuild/cpython3_3.11_pysam/build/pysam/libctabix.cpython-311-riscv64-linux-gnu.so -> /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/version.py to version.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/Pileup.py to Pileup.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/samtools.py to samtools.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/config.py to config.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/utils.py to utils.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/include/__init__.py to __init__.cpython-311.pyc byte-compiling /<>/debian/python3-pysam/usr/lib/python3.11/dist-packages/pysam/bcftools.py to bcftools.cpython-311.pyc running install_egg_info 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 -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dwz: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcf.cpython-311-riscv64-linux-gnu.so: DWARF compression not beneficial - old size 1197857 new size 1215540 dh_strip -a -O--buildsystem=pybuild debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcvcf.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 731790ddddabfd0b836de2778bec5f84df1868eb debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 6b573c602e7bf45f88a6a82e36928a6563104686 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbcftools.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 752498ba9debf6690a9be17db6bfc2b9164d0119 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcalignedsegment.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 6243db24bf91a0f4eba22ab829361fd320724acb debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcsamtools.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 ff46176d63ab46ac11f976fe8399c5e11345d7f2 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 e3ad68fc55f867e1570bf17df06d4fbd221f459c debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libchtslib.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 a02daef834251490099440106bd02cc2794d109f debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcalignmentfile.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 c4898238e71024f7a95223983bed2ceadd4ea042 42df8bce2bbc47baf022612289c68668410e19e7 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcutils.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 13cd84a906202d97c7b35ce246d47f3cefbb4284 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcbgzf.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 1234a77e82d68fb58c5d02080539f59779b705b2 debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 ae3392ed017814bb788053436206ca76e7c75def debugedit: debian/python3-pysam/usr/lib/python3/dist-packages/pysam/libctabix.cpython-311-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 c7d5e7185828986ddcf6d1b91b96540e096a36c9 dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 153 INFO: pkgstriptranslations version 153 pkgstriptranslations: processing python3-pysam (in debian/python3-pysam); do_strip: , oemstrip: pkgstriptranslations: processing python3-pysam-dbgsym (in debian/.debhelper/python3-pysam/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-pysam/DEBIAN/control, package python3-pysam, directory debian/python3-pysam pkgstripfiles: Running PNG optimization (using 8 cpus) for package python3-pysam ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.21.0+ds-1_riscv64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/python3-pysam/dbgsym-root/DEBIAN/control, package python3-pysam-dbgsym, directory debian/.debhelper/python3-pysam/dbgsym-root dpkg-deb: building package 'python3-pysam-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-pysam/python3-pysam-dbgsym_0.21.0+ds-1_riscv64.deb'. Renaming python3-pysam-dbgsym_0.21.0+ds-1_riscv64.deb to python3-pysam-dbgsym_0.21.0+ds-1_riscv64.ddeb dpkg-genbuildinfo --build=any -O../python-pysam_0.21.0+ds-1_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../python-pysam_0.21.0+ds-1_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-06-24T12:45:16Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ python-pysam_0.21.0+ds-1_riscv64.changes: ----------------------------------------- Format: 1.8 Date: Fri, 23 Jun 2023 20:10:54 +0200 Source: python-pysam Binary: python3-pysam Built-For-Profiles: noudeb Architecture: riscv64 Version: 0.21.0+ds-1 Distribution: mantic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Étienne Mollier Description: 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. Checksums-Sha1: aa9a174e58604010efdcc379b4d4d59a255eb51e 7597 python-pysam_0.21.0+ds-1_riscv64.buildinfo 51c500b8e1160c261f52bb211b535b2f2b8075ad 6899896 python3-pysam-dbgsym_0.21.0+ds-1_riscv64.ddeb 9c57b71e076e2441fe8cd3b0ae852667c0adb109 3028668 python3-pysam_0.21.0+ds-1_riscv64.deb Checksums-Sha256: 12c4cc0694baf481acbb06127670061cf4150aa6a7d93f1f8b54b3b1f7e374a5 7597 python-pysam_0.21.0+ds-1_riscv64.buildinfo b1b6bc817f0259de3614b364381c9b7960a7a2880ac511e6b47467895298f392 6899896 python3-pysam-dbgsym_0.21.0+ds-1_riscv64.ddeb 54732bbbd5c9fe95a004e4524b660db9b939729e8be4f5026cc7d8f0cd002553 3028668 python3-pysam_0.21.0+ds-1_riscv64.deb Files: f177a270b0f6513b799499d708a82649 7597 python optional python-pysam_0.21.0+ds-1_riscv64.buildinfo ca1b26dacf56f39b9e2acdebe4ef651f 6899896 debug optional python3-pysam-dbgsym_0.21.0+ds-1_riscv64.ddeb 076acc85af11dab17a5dda58604fd74b 3028668 python optional python3-pysam_0.21.0+ds-1_riscv64.deb /<>/python-pysam_0.21.0+ds-1_riscv64.changes.new could not be renamed to /<>/python-pysam_0.21.0+ds-1_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: python-pysam Binary: python3-pysam python3-pysam-dbgsym Architecture: riscv64 Version: 0.21.0+ds-1 Checksums-Md5: ca1b26dacf56f39b9e2acdebe4ef651f 6899896 python3-pysam-dbgsym_0.21.0+ds-1_riscv64.ddeb 076acc85af11dab17a5dda58604fd74b 3028668 python3-pysam_0.21.0+ds-1_riscv64.deb Checksums-Sha1: 51c500b8e1160c261f52bb211b535b2f2b8075ad 6899896 python3-pysam-dbgsym_0.21.0+ds-1_riscv64.ddeb 9c57b71e076e2441fe8cd3b0ae852667c0adb109 3028668 python3-pysam_0.21.0+ds-1_riscv64.deb Checksums-Sha256: b1b6bc817f0259de3614b364381c9b7960a7a2880ac511e6b47467895298f392 6899896 python3-pysam-dbgsym_0.21.0+ds-1_riscv64.ddeb 54732bbbd5c9fe95a004e4524b660db9b939729e8be4f5026cc7d8f0cd002553 3028668 python3-pysam_0.21.0+ds-1_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Sat, 24 Jun 2023 12:45:09 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-12), 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-riscv64-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), 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), 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), grep (= 3.8-5), groff-base (= 1.22.4-10), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 13.1.0-6ubuntu1), 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), 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), libdebconfclient0 (= 0.267ubuntu1), libdebhelper-perl (= 13.11.4ubuntu3), libdeflate-dev (= 1.15-1), libdeflate0 (= 1.15-1), libdpkg-perl (= 1.21.22ubuntu1), libdw1 (= 0.188-2.1), libelf1 (= 0.188-2.1), libexpat1 (= 2.5.0-2), libexpat1-dev (= 2.5.0-2), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-12-dev (= 12.3.0-3ubuntu1), libgcc-s1 (= 13.1.0-6ubuntu1), libgcrypt20 (= 1.10.1-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.2.1+dfsg1-1.1ubuntu1), libgnutls30 (= 3.7.9-2ubuntu1), libgomp1 (= 13.1.0-6ubuntu1), libgpg-error0 (= 1.46-1), libgssapi-krb5-2 (= 1.20.1-2), libhogweed6 (= 3.8.1-2), libhts-dev (= 1.17+ds-1), libhts3 (= 1.17+ds-1), libhtscodecs2 (= 1.5.0-1), libicu72 (= 72.1-3ubuntu2), libidn2-0 (= 2.3.3-1build1), libisl23 (= 0.26-3), libjansson4 (= 2.14-2), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-sphinxdoc (= 5.3.0-4), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libk5crypto3 (= 1.20.1-2), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-2), libkrb5support0 (= 1.20.1-2), libldap2 (= 2.6.3+dfsg-1~exp1ubuntu2), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.1-0.2), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.1.0-1), libmount1 (= 2.38.1-5ubuntu2), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.0-1), libncurses6 (= 6.4-4), libncursesw6 (= 6.4-4), libnettle8 (= 3.8.1-2), libnghttp2-14 (= 1.54.0-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libp11-kit0 (= 0.24.1-2ubuntu1), libpam-modules (= 1.5.2-6ubuntu1), libpam-modules-bin (= 1.5.2-6ubuntu1), libpam-runtime (= 1.5.2-6ubuntu1), libpam0g (= 1.5.2-6ubuntu1), libpcre2-8-0 (= 10.42-1), libperl5.36 (= 5.36.0-7ubuntu1), libpipeline1 (= 1.5.7-1), libpsl5 (= 0.21.2-1), libpython3-all-dev (= 3.11.2-1), libpython3-dev (= 3.11.2-1), libpython3-stdlib (= 3.11.2-1), libpython3.11 (= 3.11.4-1), libpython3.11-dev (= 3.11.4-1), libpython3.11-minimal (= 3.11.4-1), libpython3.11-stdlib (= 3.11.4-1), 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), 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), 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="nocheck parallel=8" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1687543854" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ python3-pysam_0.21.0+ds-1_riscv64.deb ------------------------------------- new Debian package, version 2.0. size 3028668 bytes: control archive=9143 bytes. 784 bytes, 17 lines control 34516 bytes, 352 lines md5sums 277 bytes, 12 lines * postinst #!/bin/sh 390 bytes, 12 lines * prerm #!/bin/sh Package: python3-pysam Source: python-pysam Version: 0.21.0+ds-1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 26857 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. . This package installs the module for Python 3. 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/lib/ drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/lib/python3/ drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/lib/python3/dist-packages/pysam-0.21.0.egg-info/ -rw-r--r-- root/root 1514 2023-06-23 18:10 ./usr/lib/python3/dist-packages/pysam-0.21.0.egg-info/PKG-INFO -rw-r--r-- root/root 1 2023-06-23 18:10 ./usr/lib/python3/dist-packages/pysam-0.21.0.egg-info/dependency_links.txt -rw-r--r-- root/root 1 2023-06-23 18:10 ./usr/lib/python3/dist-packages/pysam-0.21.0.egg-info/not-zip-safe -rw-r--r-- root/root 0 2023-06-23 18:10 ./usr/lib/python3/dist-packages/pysam-0.21.0.egg-info/requires.txt -rw-r--r-- root/root 6 2023-06-23 18:10 ./usr/lib/python3/dist-packages/pysam-0.21.0.egg-info/top_level.txt drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/lib/python3/dist-packages/pysam/ -rw-r--r-- root/root 8955 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/Pileup.py -rw-r--r-- root/root 3465 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/__init__.py -rw-r--r-- root/root 2078 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/bcftools.py -rw-r--r-- root/root 102 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/cbcftools_util.h -rw-r--r-- root/root 16 2023-06-23 18:10 ./usr/lib/python3/dist-packages/pysam/config.py -rw-r--r-- root/root 102 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/csamtools_util.h -rw-r--r-- root/root 3294 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/htslib_util.c -rw-r--r-- root/root 2565 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/htslib_util.h drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/lib/python3/dist-packages/pysam/include/ -rw-r--r-- root/root 0 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/__init__.py drwxr-xr-x root/root 0 2023-06-23 18:10 ./usr/lib/python3/dist-packages/pysam/include/bcftools/ -rw-r--r-- root/root 18249 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/HMM.c -rw-r--r-- root/root 18278 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/HMM.c.pysam.c -rw-r--r-- root/root 5022 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/HMM.h -rw-r--r-- root/root 2192 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/README -rw-r--r-- root/root 31831 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/abuf.c -rw-r--r-- root/root 31896 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/abuf.c.pysam.c -rw-r--r-- root/root 2521 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/abuf.h -rw-r--r-- root/root 47123 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam2bcf.c -rw-r--r-- root/root 47197 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam2bcf.c.pysam.c -rw-r--r-- root/root 8085 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam2bcf.h -rw-r--r-- root/root 28412 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam2bcf_iaux.c -rw-r--r-- root/root 28612 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -rw-r--r-- root/root 34901 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam2bcf_indel.c -rw-r--r-- root/root 35020 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -rw-r--r-- root/root 13718 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam_sample.c -rw-r--r-- root/root 13747 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam_sample.c.pysam.c -rw-r--r-- root/root 2030 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bam_sample.h -rw-r--r-- root/root 5093 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bcftools.h -rw-r--r-- root/root 1589 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bcftools.pysam.c -rw-r--r-- root/root 1876 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bcftools.pysam.h -rw-r--r-- root/root 3469 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bin.c -rw-r--r-- root/root 3498 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bin.c.pysam.c -rw-r--r-- root/root 2188 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/bin.h -rw-r--r-- root/root 5330 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/call.h -rw-r--r-- root/root 13188 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/ccall.c -rw-r--r-- root/root 13217 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/ccall.c.pysam.c -rw-r--r-- root/root 6380 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/cigar_state.h -rw-r--r-- root/root 3339 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/cols.c -rw-r--r-- root/root 3368 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/cols.c.pysam.c -rw-r--r-- root/root 1808 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/cols.h -rw-r--r-- root/root 77 2023-06-23 18:10 ./usr/lib/python3/dist-packages/pysam/include/bcftools/config.h -rw-r--r-- root/root 49995 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/consensus.c -rw-r--r-- root/root 50492 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/consensus.c.pysam.c -rw-r--r-- root/root 65349 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/convert.c -rw-r--r-- root/root 65432 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/convert.c.pysam.c -rw-r--r-- root/root 1881 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/convert.h -rw-r--r-- root/root 180840 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/csq.c -rw-r--r-- root/root 181706 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/csq.c.pysam.c -rw-r--r-- root/root 1851 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/dbuf.h -rw-r--r-- root/root 3406 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/dist.c -rw-r--r-- root/root 3435 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/dist.c.pysam.c -rw-r--r-- root/root 2850 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/dist.h -rw-r--r-- root/root 8861 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/em.c -rw-r--r-- root/root 8962 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/em.c.pysam.c -rw-r--r-- root/root 7945 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/extsort.c -rw-r--r-- root/root 7974 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/extsort.c.pysam.c -rw-r--r-- root/root 2180 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/extsort.h -rw-r--r-- root/root 144910 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/filter.c -rw-r--r-- root/root 145074 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/filter.c.pysam.c -rw-r--r-- root/root 3004 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/filter.h -rw-r--r-- root/root 8118 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/gvcf.c -rw-r--r-- root/root 8147 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/gvcf.c.pysam.c -rw-r--r-- root/root 1561 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/gvcf.h -rw-r--r-- root/root 12759 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/hclust.c -rw-r--r-- root/root 12860 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/hclust.c.pysam.c -rw-r--r-- root/root 2781 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/hclust.h -rw-r--r-- root/root 2968 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/hex.h -rw-r--r-- root/root 3163 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/khash_str2str.h -rw-r--r-- root/root 7726 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/kheap.h -rw-r--r-- root/root 7269 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/kmin.c -rw-r--r-- root/root 7298 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/kmin.c.pysam.c -rw-r--r-- root/root 1619 2023-04-01 21:14 ./usr/lib/python3/dist-packages/pysam/include/bcftools/kmin.h -rw-r--r-- root/root 9972 2023-04-01 21:14 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+------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 318188 Build-Time: 3851 Distribution: mantic-proposed Host Architecture: riscv64 Install-Time: 371 Job: python-pysam_0.21.0+ds-1.dsc Machine Architecture: riscv64 Package: python-pysam Package-Time: 4255 Source-Version: 0.21.0+ds-1 Space: 318188 Status: successful Version: 0.21.0+ds-1 -------------------------------------------------------------------------------- Finished at 2023-06-24T12:45:16Z Build needed 01:10:55, 318188k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26335199 Scanning for processes to kill in build PACKAGEBUILD-26335199 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26335199 Stopping target for build PACKAGEBUILD-26335199 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=mantic --arch=riscv64 PACKAGEBUILD-26335199 Removing build PACKAGEBUILD-26335199