Sun Jul 11 15:13:35 UTC 2021 I: starting to build libbio-db-hts-perl/bullseye/armhf on jenkins on '2021-07-11 15:13' Sun Jul 11 15:13:35 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_18/247/console.log Sun Jul 11 15:13:35 UTC 2021 I: Downloading source for bullseye/libbio-db-hts-perl=3.01-3 --2021-07-11 15:13:36-- http://cdn-fastly.deb.debian.org/debian/pool/main/libb/libbio-db-hts-perl/libbio-db-hts-perl_3.01-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2167 (2.1K) Saving to: ‘libbio-db-hts-perl_3.01-3.dsc’ 0K .. 100% 138M=0s 2021-07-11 15:13:36 (138 MB/s) - ‘libbio-db-hts-perl_3.01-3.dsc’ saved [2167/2167] Sun Jul 11 15:13:36 UTC 2021 I: libbio-db-hts-perl_3.01-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbio-db-hts-perl Binary: libbio-db-hts-perl Architecture: any Version: 3.01-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://metacpan.org/release/Bio-DB-HTS Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/libbio-db-hts-perl Vcs-Git: https://salsa.debian.org/med-team/libbio-db-hts-perl.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 12), libbio-perl-perl, libextutils-cbuilder-perl, libextutils-pkgconfig-perl, libhts-dev, libmodule-build-perl, perl Package-List: libbio-db-hts-perl deb science optional arch=any Checksums-Sha1: 292b7464e502437666907f849b8cd91465afd042 5250834 libbio-db-hts-perl_3.01.orig.tar.gz 42ca9622da41afef741df7bcc96e22370e03b6d9 3592 libbio-db-hts-perl_3.01-3.debian.tar.xz Checksums-Sha256: 12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42 5250834 libbio-db-hts-perl_3.01.orig.tar.gz e34f33c76fca3a1cbe034771bbfee3004af06a4646ec6fe799101a2ff63f2d5b 3592 libbio-db-hts-perl_3.01-3.debian.tar.xz Files: 7b7f991deddb12084cf85e0fa3d91819 5250834 libbio-db-hts-perl_3.01.orig.tar.gz ba79341d64634c06efd5b3e50d2bfcd4 3592 libbio-db-hts-perl_3.01-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl4QvAAACgkQPCZ2P2xn 5uJFzA/9G3kkeqWXkWJiSQujr64H0o7siwDCjPY33M2DPX8D3CRBa3zZbI493PcQ qXBOl0ziIE77MPM4aNZKx0vC2voLdJWRoq/flmjZK3x2HBJp0HGU2ctQxjXZPTKm teyBKSVuiEu+GqFtjEMBju9FDnQs/J63zTqQzHTfyyt+XPNiMJAwswQEikht7av4 cebU1zZcBfl7Fp+TToikAlOWAQIcET+CTUg8q7P8QW9JAl9QVgBBrlMQ2zssJvqF vV0BqZ8tR3TsoT0ylNSfhX6iR7Z3lx38o2zZUQZY7DcCEeNCUt8A8Blax7cPAvCD E3AJqbawYKKm6JzOEUzlWWu+QQOjs5ECB8Csznd2NIQlu9z/RNk1G90wvAN1C5h2 /xF/uDqzAjUXr+P8TBH0m9DPO4GjTJb4A8Gh3EzHAEfW/1HfpaKKMnoV+c6vb3EZ /tZV+UywgXvLyG5jxw4lluXweatTsdbM8Q5qSenufdPWFhw5Ke+3UM0KEwnwCkMH Vk3kiJ//bQ6E463IlZQ2rrO8n1yW5f0i+2T3kx6vgfVtyfaWV3yQEIawXBtacFmG 9F1nBJDXWiYXO/J6RQVScdMEX5hy91K1jjE8a8SvEOHQdhrf7UePWduN7leghExb q2J9Z8IDKceZvr2pPSDjGkcPPIaR4iYIvi1BX9DoxxrqR5Vd5SM= =pV7J -----END PGP SIGNATURE----- Sun Jul 11 15:13:36 UTC 2021 I: Checking whether the package is not for us Sun Jul 11 15:13:36 UTC 2021 I: Starting 1st build on remote node ff64a-armhf-rb.debian.net. Sun Jul 11 15:13:36 UTC 2021 I: Preparing to do remote build '1' on ff64a-armhf-rb.debian.net. Sun Jul 11 15:17:01 UTC 2021 I: Deleting $TMPDIR on ff64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 11 03:13:43 -12 2021 I: pbuilder-time-stamp: 1626016423 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libbio-db-hts-perl_3.01-3.dsc] I: copying [./libbio-db-hts-perl_3.01.orig.tar.gz] I: copying [./libbio-db-hts-perl_3.01-3.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.kC4WT5GC/trustedkeys.kbx': General error gpgv: Signature made Sat Jan 4 04:23:28 2020 -12 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libbio-db-hts-perl_3.01-3.dsc dpkg-source: info: extracting libbio-db-hts-perl in libbio-db-hts-perl-3.01 dpkg-source: info: unpacking libbio-db-hts-perl_3.01.orig.tar.gz dpkg-source: info: unpacking libbio-db-hts-perl_3.01-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying find_htslib.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/15021/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=5' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='cb84a58846384ec0b35b86fff1cc57a6' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='15021' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.q6dILiHBrt/pbuilderrc_7ZVT --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.q6dILiHBrt/b1 --logfile b1/build.log libbio-db-hts-perl_3.01-3.dsc' SUDO_GID='114' SUDO_UID='109' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux ff64a 5.10.0-7-arm64 #1 SMP Debian 5.10.40-1 (2021-05-28) aarch64 GNU/Linux I: ls -l /bin total 3580 -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash -rwxr-xr-x 1 root root 75880 Sep 22 2020 date -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd -rwxr-xr-x 1 root root 59912 Sep 22 2020 df -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir -rwxr-xr-x 1 root root 55012 Feb 7 02:38 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 22496 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln -rwxr-xr-x 1 root root 35068 Feb 7 2020 login -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 9 21:28 sh -> dash -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch -rwxr-xr-x 1 root root 22496 Sep 22 2020 true -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir -rwxr-xr-x 1 root root 38512 Feb 7 02:38 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew I: user script /srv/workspace/pbuilder/15021/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), libbio-perl-perl, libextutils-cbuilder-perl, libextutils-pkgconfig-perl, libhts-dev, libmodule-build-perl, perl dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19398 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libextutils-pkgconfig-perl; however: Package libextutils-pkgconfig-perl is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libmodule-build-perl; however: Package libmodule-build-perl is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbio-perl-perl{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdata-stag-perl{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libextutils-pkgconfig-perl{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libhts-dev{a} libhts3{a} libicu67{a} libio-string-perl{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmodule-build-perl{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bioperl-run ca-certificates curl libace-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libbio-perl-run-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgd-perl libglib2.0-data libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libldap-common liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libmodule-signature-perl libpod-readme-perl libpostscript-perl libsasl2-modules libset-scalar-perl libsoap-lite-perl libsoftware-license-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx perl-tk publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 54 newly installed, 0 to remove and 0 not upgraded. Need to get 28.6 MB of archives. After unpacking 86.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-7 [138 kB] Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB] Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB] Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB] Get: 6 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB] Get: 9 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB] Get: 11 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB] Get: 13 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 23 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB] Get: 25 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB] Get: 26 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB] Get: 27 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB] Get: 28 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB] Get: 29 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main armhf libio-string-perl all 1.08-3.1 [11.8 kB] Get: 33 http://deb.debian.org/debian bullseye/main armhf libdata-stag-perl all 0.14-2 [448 kB] Get: 34 http://deb.debian.org/debian bullseye/main armhf libbio-perl-perl all 1.7.7-2 [2607 kB] Get: 35 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB] Get: 36 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1 [67.6 kB] Get: 37 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1 [99.1 kB] Get: 38 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3 [210 kB] Get: 39 http://deb.debian.org/debian bullseye/main armhf libnghttp2-14 armhf 1.43.0-1 [65.6 kB] Get: 40 http://deb.debian.org/debian bullseye/main armhf libpsl5 armhf 0.21.0-1.2 [56.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 42 http://deb.debian.org/debian bullseye/main armhf libssh2-1 armhf 1.9.0-2 [143 kB] Get: 43 http://deb.debian.org/debian bullseye/main armhf libcurl3-gnutls armhf 7.74.0-1.3+b1 [306 kB] Get: 44 http://deb.debian.org/debian bullseye/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3+b1 [402 kB] Get: 45 http://deb.debian.org/debian bullseye/main armhf libdeflate0 armhf 1.7-1 [43.1 kB] Get: 46 http://deb.debian.org/debian bullseye/main armhf libdeflate-dev armhf 1.7-1 [39.9 kB] Get: 47 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB] Get: 48 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB] Get: 49 http://deb.debian.org/debian bullseye/main armhf libextutils-pkgconfig-perl all 1.16-1.1 [10.9 kB] Get: 50 http://deb.debian.org/debian bullseye/main armhf libhts3 armhf 1.11-4 [332 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf liblzma-dev armhf 5.2.5-2 [220 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB] Get: 53 http://deb.debian.org/debian bullseye/main armhf libhts-dev armhf 1.11-4 [3819 kB] Get: 54 http://deb.debian.org/debian bullseye/main armhf libmodule-build-perl all 0.423100-1 [258 kB] Fetched 28.6 MB in 3s (10.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. 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Reading state information... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/libbio-db-hts-perl-3.01/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbio-db-hts-perl_3.01-3_source.changes dpkg-buildpackage: info: source package libbio-db-hts-perl dpkg-buildpackage: info: source version 3.01-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure perl Build.PL --installdirs vendor --config "optimize=-g -O2 -fdebug-prefix-map=/build/libbio-db-hts-perl-3.01=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/build/libbio-db-hts-perl-3.01=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now" Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '3.01' dh_auto_build perl Build Building Bio-DB-HTS arm-linux-gnueabihf-gcc -I/usr/lib/arm-linux-gnueabihf/perl/5.32/CORE -DVERSION="3.01" -DXS_VERSION="3.01" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/libbio-db-hts-perl-3.01=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/libbio-db-hts-perl-3.01=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c lib/Bio/DB/HTS.xs: In function 'XS_Bio__DB__HTS__VCF__Header_fmt_text': lib/Bio/DB/HTS.xs:1769:5: warning: 'bcf_hdr_fmt_text' is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 1769 | RETVAL = newSVpv(bcf_hdr_fmt_text(header, is_bcf, &len), 0); | ^~~~~~ In file included from lib/Bio/DB/HTS.xs:59: /usr/include/htslib/vcf.h:570:11: note: declared here 570 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) | ^~~~~~~~~~~~~~~~ lib/Bio/DB/HTS.xs: In function 'XS_Bio__DB__HTS__VCF__Row_print': lib/Bio/DB/HTS.xs:1785:13: warning: format '%d' expects argument of type 'int', but argument 2 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=] 1785 | printf("position:%d\t", (row->pos+1)); | ^~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | hts_pos_t {aka long long int} ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs') arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/build/libbio-db-hts-perl-3.01=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -lhts -lpthread -lz arm-linux-gnueabihf-gcc -I/usr/lib/arm-linux-gnueabihf/perl/5.32/CORE -DVERSION="3.01" -DXS_VERSION="3.01" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O2 -fdebug-prefix-map=/build/libbio-db-hts-perl-3.01=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/libbio-db-hts-perl-3.01=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c In file included from /usr/lib/arm-linux-gnueabihf/perl/5.32/CORE/perl.h:5606, from lib/Bio/DB/HTS/Faidx.xs:18: lib/Bio/DB/HTS/Faidx.xs: In function 'new': lib/Bio/DB/HTS/Faidx.xs:51:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 51 | obj = newSViv((IV)faidx); | ^ /usr/lib/arm-linux-gnueabihf/perl/5.32/CORE/embed.h:376:40: note: in definition of macro 'newSViv' 376 | #define newSViv(a) Perl_newSViv(aTHX_ a) | ^ lib/Bio/DB/HTS/Faidx.xs: In function 'get_sequence': lib/Bio/DB/HTS/Faidx.xs:68:10: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 68 | fai = ((Faidx*)SvIV(SvRV(obj)))->index; | ^ lib/Bio/DB/HTS/Faidx.xs: In function 'get_sequence2': lib/Bio/DB/HTS/Faidx.xs:87:10: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 87 | fai = ((Faidx*)SvIV(SvRV(obj)))->index; | ^ lib/Bio/DB/HTS/Faidx.xs: In function 'has_sequence': lib/Bio/DB/HTS/Faidx.xs:102:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 102 | has_seq = faidx_has_seq(((Faidx*)SvIV(SvRV(obj)))->index, SvPV(seq_id, PL_na)); | ^ lib/Bio/DB/HTS/Faidx.xs: In function 'length': lib/Bio/DB/HTS/Faidx.xs:110:21: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 110 | faidx_t *fai = ((Faidx*)SvIV(SvRV(obj)))->index ; | ^ lib/Bio/DB/HTS/Faidx.xs: In function 'DESTROY': lib/Bio/DB/HTS/Faidx.xs:118:18: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 118 | Faidx* faidx = (Faidx*)SvIV(SvRV(obj)); | ^ lib/Bio/DB/HTS/Faidx.xs: In function 'XS_Bio__DB__HTS__Faidx_get_all_sequence_ids': lib/Bio/DB/HTS/Faidx.xs:198:21: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 198 | faidx_t *fai = ((Faidx*)SvIV(SvRV(obj)))->index ; | ^ ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs') arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/build/libbio-db-hts-perl-3.01=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -lhts -lpthread -lz dh_auto_test perl Build test --verbose 1 t/00load.t ....... ok 1 - use Bio::DB::HTS; ok 2 - use Bio::DB::HTS::Tabix; ok 3 - use Bio::DB::HTS::Tabix::Iterator; ok 4 - use Bio::DB::HTS::Kseq; 1..4 ok t/01bam.t ........ 1..452 # Running under perl version 5.032001 for linux # Current time local: Sun Jul 11 03:15:45 2021 # Current time GMT: Sun Jul 11 15:15:45 2021 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 ok 251 ok 252 ok 253 ok 254 ok 255 ok 256 ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 ok 268 ok 269 ok 270 ok 271 ok 272 ok 273 ok 274 ok 275 ok 276 ok 277 ok 278 ok 279 ok 280 ok 281 ok 282 ok 283 ok 284 ok 285 ok 286 ok 287 ok 288 ok 289 ok 290 ok 291 ok 292 ok 293 ok 294 ok 295 ok 296 ok 297 ok 298 ok 299 ok 300 ok 301 ok 302 ok 303 ok 304 ok 305 ok 306 ok 307 ok 308 ok 309 ok 310 ok 311 ok 312 ok 313 ok 314 ok 315 ok 316 ok 317 ok 318 ok 319 ok 320 ok 321 ok 322 ok 323 ok 324 ok 325 ok 326 ok 327 ok 328 ok 329 ok 330 ok 331 ok 332 ok 333 ok 334 ok 335 ok 336 ok 337 ok 338 ok 339 ok 340 ok 341 ok 342 ok 343 ok 344 ok 345 ok 346 ok 347 ok 348 ok 349 ok 350 ok 351 ok 352 ok 353 ok 354 ok 355 ok 356 ok 357 ok 358 ok 359 ok 360 ok 361 ok 362 ok 363 ok 364 ok 365 ok 366 ok 367 ok 368 ok 369 ok 370 ok 371 ok 372 ok 373 ok 374 ok 375 ok 376 ok 377 ok 378 ok 379 ok 380 ok 381 ok 382 ok 383 ok 384 ok 385 ok 386 ok 387 ok 388 ok 389 ok 390 ok 391 ok 392 ok 393 ok 394 ok 395 ok 396 ok 397 ok 398 ok 399 ok 400 ok 401 ok 402 ok 403 ok 404 ok 405 ok 406 ok 407 ok 408 ok 409 ok 410 ok 411 ok 412 ok 413 ok 414 ok 415 ok 416 ok 417 ok 418 ok 419 ok 420 ok 421 ok 422 ok 423 ok 424 ok 425 ok 426 ok 427 ok 428 ok 429 ok 430 ok 431 ok 432 ok 433 ok 434 ok 435 ok 436 ok 437 ok 438 ok 439 ok 440 ok 441 ok 442 ok 443 ok 444 ok 445 ok 446 ok 447 ok 448 ok 449 ok 450 ok 451 ok 452 ok t/02faidx.t ...... 1..15 ok 1 - use Bio::DB::HTS; ok 2 - use Bio::DB::HTS::Faidx; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 # 230218 ok 13 - length of I ok 14 - has sequence I ok 15 - Does not have sequence II ok t/03cram.t ....... 1..139 # Running under perl version 5.032001 for linux # Current time local: Sun Jul 11 03:15:53 2021 # Current time GMT: Sun Jul 11 15:15:53 2021 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok t/04tabix.t ...... 1..21 ok 1 - use Bio::DB::HTS::Tabix; ok 2 - \#CHROM FROM TO GERP ok 3 - \#CHROM FROM TO GERP ok 4 - can query a region ok 5 - can get a value from the iterator ok 6 - row value is correct ok 7 - correct number of values come back from the iterator ok 8 - A reference of type 'ARRAY' isa 'ARRAY' ok 9 - seqnames are correct ok 10 - can query a region with ':' in chr ok 11 - can get a value from the iterator ok 12 - row value is correct with ':' in chr ok 13 - can query a region with ':' in chr, no end ok 14 - can get a value from the iterator ok 15 - row value is correct with ':' in chr, no end ok 16 - can query a region with ':' in chr, no coord ok 17 - can get a value from the iterator ok 18 - row value is correct with ':' in chr, no coord ok 19 - querying non existent chrom ok 20 - \#\#fileformat=VCFv4.2 ok 21 - \#\#reference=human_b36_both.fasta ok t/05vcf.t ........ 1..177 ok 1 - use Bio::DB::HTS::VCF; ok 2 - use Bio::DB::HTS::VCF::Row; ok 3 - use Bio::DB::HTS::VCF::RowPtr; ok 4 - use Bio::DB::HTS::VCF::Header; ok 5 - use Bio::DB::HTS::VCF::HeaderPtr; ok 6 - Chromosome value read ok 7 - Chromosome value read ok 8 - Position value read ok 9 - Quality value read ok 10 - Quality value read ok 11 - ID value read ok 12 - Number of alleles value read ok 13 - A reference of type 'ARRAY' isa 'ARRAY' ok 14 - alleles are correct ok 15 - VCF file open ok 16 - correct number of variants identified in file ok 17 - Header formatted string ok 18 - VCF Header version matches ok 19 - Number of samples ok 20 - sample names correct ok 21 - Number of seqnames ok 22 ok 23 - sequence names correct ok 24 - Next row ok 25 - Chromosome value read ok 26 - Position value read ok 27 - ID value read ok 28 - Num Filters OK ok 29 - Actual Filter present ok 30 - PASS filter absent ok 31 - Variant type matches ok 32 - info read correctly ok 33 - A reference of type 'ARRAY' isa 'ARRAY' ok 34 - info flag read correctly ok 35 - info flag type correct ok 36 - A reference of type 'ARRAY' isa 'ARRAY' ok 37 - info float read correctly ok 38 - info float type correct ok 39 - A reference of type 'ARRAY' isa 'ARRAY' ok 40 - info string read correctly ok 41 - info String type correct ok 42 - A reference of type 'ARRAY' isa 'ARRAY' ok 43 - info ints read correctly ok 44 - info int type correct ok 45 - format int read ok 46 - format int read ok 47 - format id not present ok 48 - format read ok 49 - Next row ok 50 - Chromosome value read ok 51 - Position value read ok 52 - Quality value read ok 53 - Reference value read ok 54 - Num Alleles ok 55 - Is SNP ok 56 - A reference of type 'ARRAY' isa 'ARRAY' ok 57 - alleles are correct ok 58 - Num Filters OK ok 59 - PASS Filter present ok 60 - Actual Filter absent ok 61 - Made up filter not existing ok 62 - info read correctly ok 63 - format int read ok 64 - format int read ok 65 - format id not present ok 66 - format read ok 67 - Next row ok 68 - Chromosome value read ok 69 - int format type correct ok 70 - format int read ok 71 - format int read ok 72 - format int read # !!! Not sure this is correct !!! ok 73 - format int read ok 74 - format read ok 75 - A reference of type 'ARRAY' isa 'ARRAY' ok 76 - genotypes read correctly ok 77 - format id not found ok 78 - info id not found ok 79 - info read correctly ok 80 - can query a region ok 81 - can get a value from the iterator ok 82 - chr ok 83 - position ok 84 - id ok 85 - reference ok 86 - info ok 87 - info ok 88 - info ok 89 - info ok 90 - can get a value from the iterator ok 91 - chr ok 92 - position ok 93 - id ok 94 - reference ok 95 - info ok 96 - no more results ok 97 - BCF file open ok 98 - correct number of variants identified in file ok 99 - Header formatted string ok 100 - VCF Header version matches ok 101 - Number of samples ok 102 - sample names correct ok 103 - Number of seqnames ok 104 - sequence names correct ok 105 - Next row ok 106 - Chromosome value read ok 107 - Position value read ok 108 - ID value read ok 109 - Num Filters OK ok 110 - Actual Filter present ok 111 - PASS filter absent ok 112 - Variant type matches ok 113 - info read correctly ok 114 - A reference of type 'ARRAY' isa 'ARRAY' ok 115 - info flag read correctly ok 116 - info flag type correct ok 117 - A reference of type 'ARRAY' isa 'ARRAY' ok 118 - info float read correctly ok 119 - info float type correct ok 120 - A reference of type 'ARRAY' isa 'ARRAY' ok 121 - info string read correctly ok 122 - info String type correct ok 123 - A reference of type 'ARRAY' isa 'ARRAY' ok 124 - info ints read correctly ok 125 - info int type correct ok 126 - format int read ok 127 - format int read ok 128 - format ID not present ok 129 - format read ok 130 - Next row ok 131 - Chromosome value read ok 132 - Position value read ok 133 - Quality value read ok 134 - Reference value read ok 135 - Num Alleles ok 136 - Is SNP ok 137 - A reference of type 'ARRAY' isa 'ARRAY' ok 138 - alleles are correct ok 139 - Num Filters OK ok 140 - PASS Filter present ok 141 - Actual Filter absent ok 142 - Made up filter not existing ok 143 - info read correctly ok 144 - format int read ok 145 - format int read ok 146 - format ID not present ok 147 - format read ok 148 - Next row ok 149 - Chromosome value read ok 150 - int format type correct ok 151 - format int read ok 152 - format int read ok 153 - format int read # !!! Not sure this is correct !!! ok 154 - format int read ok 155 - format read ok 156 - A reference of type 'ARRAY' isa 'ARRAY' ok 157 - genotypes read correctly ok 158 - format id not found ok 159 - info id not found ok 160 - info read correctly ok 161 - can query a region ok 162 - can get a value from the iterator ok 163 - chr ok 164 - position ok 165 - id ok 166 - reference ok 167 - info ok 168 - info ok 169 - info ok 170 - info ok 171 - can get a value from the iterator ok 172 - chr ok 173 - position ok 174 - id ok 175 - reference ok 176 - info ok 177 - no more results ok t/06kseq.t ....... ok 1 - correct num. seqs in bug2335 ok 2 - sample sequence obtained ok 3 - seq matches bug2335 ok 4 - desc matches bug2335 ok 5 - name matches bug2335 ok 6 - qual matches bug2335 ok 7 - Checking qual and seq lengths are the same in bug2335 ok 8 - Checking qual and seq lengths are the same using object methods in bug2335 ok 9 - correct num. seqs in evil_wrapping ok 10 - sample sequence obtained ok 11 - seq matches evil_wrapping ok 12 - desc matches evil_wrapping ok 13 - name matches evil_wrapping ok 14 - qual matches evil_wrapping ok 15 - Checking qual and seq lengths are the same in evil_wrapping ok 16 - Checking qual and seq lengths are the same using object methods in evil_wrapping ok 17 - correct num. seqs in example ok 18 - sample sequence obtained ok 19 - seq matches example ok 20 - desc matches example ok 21 - name matches example ok 22 - qual matches example ok 23 - Checking qual and seq lengths are the same in example ok 24 - Checking qual and seq lengths are the same using object methods in example ok 25 - correct num. seqs in illumina_faked ok 26 - sample sequence obtained ok 27 - seq matches illumina_faked ok 28 - desc matches illumina_faked ok 29 - name matches illumina_faked ok 30 - qual matches illumina_faked ok 31 - Checking qual and seq lengths are the same in illumina_faked ok 32 - Checking qual and seq lengths are the same using object methods in illumina_faked ok 33 - correct num. seqs in sanger_93 ok 34 - sample sequence obtained ok 35 - seq matches sanger_93 ok 36 - desc matches sanger_93 ok 37 - name matches sanger_93 ok 38 - qual matches sanger_93 ok 39 - Checking qual and seq lengths are the same in sanger_93 ok 40 - Checking qual and seq lengths are the same using object methods in sanger_93 ok 41 - correct num. seqs in sanger_faked ok 42 - sample sequence obtained ok 43 - seq matches sanger_faked ok 44 - desc matches sanger_faked ok 45 - name matches sanger_faked ok 46 - qual matches sanger_faked ok 47 - Checking qual and seq lengths are the same in sanger_faked ok 48 - Checking qual and seq lengths are the same using object methods in sanger_faked ok 49 - correct num. seqs in solexa_example ok 50 - sample sequence obtained ok 51 - seq matches solexa_example ok 52 - desc matches solexa_example ok 53 - name matches solexa_example ok 54 - qual matches solexa_example ok 55 - Checking qual and seq lengths are the same in solexa_example ok 56 - Checking qual and seq lengths are the same using object methods in solexa_example ok 57 - correct num. seqs in solexa_faked ok 58 - sample sequence obtained ok 59 - seq matches solexa_faked ok 60 - desc matches solexa_faked ok 61 - name matches solexa_faked ok 62 - qual matches solexa_faked ok 63 - Checking qual and seq lengths are the same in solexa_faked ok 64 - Checking qual and seq lengths are the same using object methods in solexa_faked ok 65 - correct num. seqs in test1_sanger ok 66 - sample sequence obtained ok 67 - seq matches test1_sanger ok 68 - desc matches test1_sanger ok 69 - name matches test1_sanger ok 70 - qual matches test1_sanger ok 71 - Checking qual and seq lengths are the same in test1_sanger ok 72 - Checking qual and seq lengths are the same using object methods in test1_sanger ok 73 - correct num. seqs in test2_solexa ok 74 - sample sequence obtained ok 75 - seq matches test2_solexa ok 76 - desc matches test2_solexa ok 77 - name matches test2_solexa ok 78 - qual matches test2_solexa ok 79 - Checking qual and seq lengths are the same in test2_solexa ok 80 - Checking qual and seq lengths are the same using object methods in test2_solexa ok 81 - correct num. seqs in test3_illumina ok 82 - sample sequence obtained ok 83 - seq matches test3_illumina ok 84 - desc matches test3_illumina ok 85 - name matches test3_illumina ok 86 - qual matches test3_illumina ok 87 - Checking qual and seq lengths are the same in test3_illumina ok 88 - Checking qual and seq lengths are the same using object methods in test3_illumina ok 89 - correct num. seqs in tricky ok 90 - sample sequence obtained ok 91 - seq matches tricky ok 92 - desc matches tricky ok 93 - name matches tricky ok 94 - qual matches tricky ok 95 - Checking qual and seq lengths are the same in tricky ok 96 - Checking qual and seq lengths are the same using object methods in tricky ok 97 - correct num. seqs in zero_qual ok 98 - sample sequence obtained ok 99 - seq matches zero_qual ok 100 - desc matches zero_qual ok 101 - name matches zero_qual ok 102 - qual matches zero_qual ok 103 - Checking qual and seq lengths are the same in zero_qual ok 104 - Checking qual and seq lengths are the same using object methods in zero_qual 1..104 ok [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Protocol not supported t/07cramwrite.t .. 1..22 # Running under perl version 5.032001 for linux # Current time local: Sun Jul 11 03:16:28 2021 # Current time GMT: Sun Jul 11 15:16:28 2021 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok t/08bamwrite.t ... 1..22 # Running under perl version 5.032001 for linux # Current time local: Sun Jul 11 03:16:29 2021 # Current time GMT: Sun Jul 11 15:16:29 2021 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok t/09sam.t ........ ok 1 ok 2 # skip Cannot test header reading for htslib < 1.5 ok 3 # skip Cannot test header reading for htslib < 1.5 ok 4 # skip Cannot test header reading for htslib < 1.5 ok 5 # skip Cannot test header reading for htslib < 1.5 ok 6 # skip Cannot test header reading for htslib < 1.5 ok 7 # skip Cannot test header reading for htslib < 1.5 ok 8 # skip Cannot test header reading for htslib < 1.5 ok 9 # skip Cannot test header reading for htslib < 1.5 ok 10 # skip Cannot test header reading for htslib < 1.5 ok 11 # skip Cannot test header reading for htslib < 1.5 ok 12 ok 13 ok 14 # skip Cannot test iterating over alignments for htslib < 1.5 ok 15 # skip Cannot test iterating over alignments for htslib < 1.5 ok 16 # skip Cannot test iterating over alignments for htslib < 1.5 ok 17 # skip Cannot test iterating over alignments for htslib < 1.5 ok 18 ok 19 ok 20 ok 21 ok 22 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' ok 23 1..23 ok t/10leak.t ....... skipped: require Test::LeakTrace All tests successful. Files=11, Tests=979, 48 wallclock secs ( 0.52 usr 0.08 sys + 46.34 cusr 2.04 csys = 48.98 CPU) Result: PASS create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install perl Build install --destdir /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl --create_packlist 0 Building Bio-DB-HTS Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/auto/Bio/DB/HTS/HTS.so Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/auto/Bio/DB/HTS/HTS.bs Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/auto/Bio/DB/HTS/Faidx/Faidx.bs Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/auto/Bio/DB/HTS/Faidx/Faidx.so Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Query.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Segment.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Kseq.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/VCF.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Pileup.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Tabix.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/PileupWrapper.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/AlignWrapper.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Faidx.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Constants.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/ReadIterator.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/FetchIterator.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Alignment.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Target.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Kseq/Iterator.pod Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Kseq/Record.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/VCF/RowPtr.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/VCF/Header.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/VCF/Iterator.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/VCF/HeaderPtr.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/VCF/Row.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/lib/arm-linux-gnueabihf/perl5/5.32/Bio/DB/HTS/Tabix/Iterator.pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Segment.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::AlignWrapper.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Tabix::Iterator.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Pileup.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Query.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::PileupWrapper.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Tabix.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::ReadIterator.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq::Record.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::VCF.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq::Iterator.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::FetchIterator.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Faidx.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Target.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Constants.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Alignment.3pm Installing /build/libbio-db-hts-perl-3.01/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::VCF::Iterator.3pm dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbio-db-hts-perl-dbgsym' in '../libbio-db-hts-perl-dbgsym_3.01-3_armhf.deb'. dpkg-deb: building package 'libbio-db-hts-perl' in '../libbio-db-hts-perl_3.01-3_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libbio-db-hts-perl_3.01-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/15021 and its subdirectories I: Current time: Sun Jul 11 03:16:55 -12 2021 I: pbuilder-time-stamp: 1626016615 Sun Jul 11 15:17:03 UTC 2021 I: 1st build successful. Starting 2nd build on remote node virt32a-armhf-rb.debian.net. Sun Jul 11 15:17:03 UTC 2021 I: Preparing to do remote build '2' on virt32a-armhf-rb.debian.net. Sun Jul 11 15:22:13 UTC 2021 I: Deleting $TMPDIR on virt32a-armhf-rb.debian.net. Sun Jul 11 15:22:15 UTC 2021 I: libbio-db-hts-perl_3.01-3_armhf.changes: Format: 1.8 Date: Fri, 03 Jan 2020 22:21:07 +0100 Source: libbio-db-hts-perl Binary: libbio-db-hts-perl libbio-db-hts-perl-dbgsym Architecture: armhf Version: 3.01-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: libbio-db-hts-perl - Perl interface to the HTS library Changes: libbio-db-hts-perl (3.01-3) unstable; urgency=medium . * Team upload. * Fix tests with missing dependencies. (Closes #948097) * Multi-Arch: same Checksums-Sha1: ecb8c2855b286c6314fd1f8cf1ffc8a9c9ed21bc 146336 libbio-db-hts-perl-dbgsym_3.01-3_armhf.deb 987a6d43b534181fb9b568fa9a02ca1f0ee77869 5741 libbio-db-hts-perl_3.01-3_armhf.buildinfo a8958f005e4ffba545f1b0ffb0c948a2cf1f0f10 153000 libbio-db-hts-perl_3.01-3_armhf.deb Checksums-Sha256: d8683f49763743efd41db90951e73cd7c7a143f9a9740e79e02dcb5bd1c8cec6 146336 libbio-db-hts-perl-dbgsym_3.01-3_armhf.deb 298bc91fd7070375b0b2a89848f001730f1467a3b56c636d192e07fb80733db2 5741 libbio-db-hts-perl_3.01-3_armhf.buildinfo 8dcd2793115bba3cf17372018071e829d4484e56c3df61e03c591c99af711810 153000 libbio-db-hts-perl_3.01-3_armhf.deb Files: e5c0a4a097eef028b0397e3739cc103d 146336 debug optional libbio-db-hts-perl-dbgsym_3.01-3_armhf.deb af0ad8e4fe79be12cb1f3d65a6f3aad8 5741 science optional libbio-db-hts-perl_3.01-3_armhf.buildinfo 975b972d47ea67f85f3de62a8bf53313 153000 science optional libbio-db-hts-perl_3.01-3_armhf.deb Sun Jul 11 15:22:16 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.q6dILiHBrt/libbio-db-hts-perl_3.01-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.q6dILiHBrt/libbio-db-hts-perl_3.01-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.q6dILiHBrt/libbio-db-hts-perl_3.01-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.q6dILiHBrt/b1/libbio-db-hts-perl_3.01-3_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.q6dILiHBrt/b2/libbio-db-hts-perl_3.01-3_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.298s) 0.298s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.025s) 0.025s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Jul 11 15:22:18 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Sun Jul 11 15:22:18 UTC 2021 I: libbio-db-hts-perl from bullseye built successfully and reproducibly on armhf. Sun Jul 11 15:22:19 UTC 2021 I: Submitting .buildinfo files to external archives: Sun Jul 11 15:22:19 UTC 2021 I: Submitting 8.0K b1/libbio-db-hts-perl_3.01-3_armhf.buildinfo.asc Sun Jul 11 15:22:20 UTC 2021 I: Submitting 8.0K b2/libbio-db-hts-perl_3.01-3_armhf.buildinfo.asc Sun Jul 11 15:22:22 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jul 11 15:22:22 UTC 2021 I: Done submitting .buildinfo files. Sun Jul 11 15:22:22 UTC 2021 I: Removing signed libbio-db-hts-perl_3.01-3_armhf.buildinfo.asc files: removed './b1/libbio-db-hts-perl_3.01-3_armhf.buildinfo.asc' removed './b2/libbio-db-hts-perl_3.01-3_armhf.buildinfo.asc'