Fri Dec 13 05:03:53 UTC 2024 I: starting to build allelecount/trixie/arm64 on jenkins on '2024-12-13 05:03' Fri Dec 13 05:03:53 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/49155/console.log Fri Dec 13 05:03:53 UTC 2024 I: Downloading source for trixie/allelecount=4.3.0-3 Fri Dec 13 05:03:53 UTC 2024 E: Download of allelecount=4.3.0-3 sources (for trixie) failed. Fri Dec 13 05:03:53 UTC 2024 E: Sleeping 5m before re-trying... Fri Dec 13 05:08:54 UTC 2024 I: Downloading source for trixie/allelecount=4.3.0-3 --2024-12-13 05:08:54-- http://deb.debian.org/debian/pool/main/a/allelecount/allelecount_4.3.0-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2409 (2.4K) [text/prs.lines.tag] Saving to: ‘allelecount_4.3.0-3.dsc’ 0K .. 100% 276M=0s 2024-12-13 05:08:54 (276 MB/s) - ‘allelecount_4.3.0-3.dsc’ saved [2409/2409] Fri Dec 13 05:08:54 UTC 2024 I: allelecount_4.3.0-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: allelecount Binary: allelecount, liballelecount-perl Architecture: any all Version: 4.3.0-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/cancerit/alleleCount Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/allelecount Vcs-Git: https://salsa.debian.org/med-team/allelecount.git Testsuite: autopkgtest, autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13), libhts-dev, libbz2-dev, libconst-fast-perl , libdevel-cover-perl , libfile-slurp-perl , libfile-which-perl , libipc-system-simple-perl , libjson-perl , libpod-coverage-perl , libtest-fatal-perl , libtry-tiny-perl , perl Package-List: allelecount deb science optional arch=any liballelecount-perl deb perl optional arch=all Checksums-Sha1: c2e81c130d21010097c4e304d46881f808bf7123 1390569 allelecount_4.3.0.orig.tar.gz 8ce5e32027ba0035ec6b911717e5431ddfbdfc1a 16284 allelecount_4.3.0-3.debian.tar.xz Checksums-Sha256: 5363ae12c2385c962728336a4498b1a29c9eaa3d4a24492d0debf897771cfd3c 1390569 allelecount_4.3.0.orig.tar.gz 4e2b1dff61b8c788d23bfe68c5d9da3cbc2bbda07722292979844a382adc0737 16284 allelecount_4.3.0-3.debian.tar.xz Files: 331975437e661cab1a950c3b3d2cc5c2 1390569 allelecount_4.3.0.orig.tar.gz c502a342cbf0a47e917195dbba8b23f4 16284 allelecount_4.3.0-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmdYa30RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGIyA//arqKPufJ/W5SUy2ygPsuR31N1cRwMs38 x+sfUcis3ZSmz7wjtRyOW79JKxX/dazzaYiVTLrKfyeUkOPr4I6zS82CFR0qcqUJ dfHoD/6up2F/d0It4NVHLstPVGVr1nv+f0MW3L7ZrLvfRlxxRsngzlkEgh1e2VkN fBFMketCOf8QS4HtJwAXNz81o0gnqTXQ9xivgUt6IG/gX+jsudfWPj2z5YKiUMO9 NJgJWjsGIsAuCxotOy/zGkCOJTLP2LiQJceAQ1GGH3fV6cMn6tX3lBmYK4O5EBWH 6Z6nHbb3ZPNHPWzK9UetWP8M8+zQxMEr2jAJJFjrxwfrQcfuhRpnsGNlX1ewWWqi x73CDmVi4iLt/zGOezwh65aBqpI3rSsYzjkV3u+h9SNBkPgSRZgXfoUekaPK31ZV HiU9jDYtOOX5mNRiEYZtyUHb+i9rnJ0JcO1bEy62paJibUix76XG8BxJlEWZFtLS 5RKpl5nx2WOSv8h+wMRQ2+2qJfAPMlCgAvFXvDpQbQfgXUxn0MsGGuBkJqgm3L7p DGFs+BqfsMeD+M4/SJ4QzdemdFBhPQx3AoCJ2SJH6pZXoQc9a4p3Jtuev/7b41q1 cXjMyPrJlFq+cVwWua5C11wjr4zlXdaLDyTICjGC+pj1HskhfJGXcSob47kQZWEl Y2twcSopH4s= =uSbc -----END PGP SIGNATURE----- Fri Dec 13 05:08:54 UTC 2024 I: Checking whether the package is not for us Fri Dec 13 05:08:54 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Fri Dec 13 05:08:54 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Fri Dec 13 05:09:35 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 12 17:08:56 -12 2024 I: pbuilder-time-stamp: 1734066536 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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 [allelecount_4.3.0-3.dsc] I: copying [./allelecount_4.3.0.orig.tar.gz] I: copying [./allelecount_4.3.0-3.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Dec 10 16:25:33 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./allelecount_4.3.0-3.dsc: no acceptable signature found dpkg-source: info: extracting allelecount in allelecount-4.3.0 dpkg-source: info: unpacking allelecount_4.3.0.orig.tar.gz dpkg-source: info: unpacking allelecount_4.3.0-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/645684/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='bae2061618b94e2db114bcd4a11e1c12' 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='645684' 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/r-b-build.yOy30I5m/pbuilderrc_21AQ --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yOy30I5m/b1 --logfile b1/build.log allelecount_4.3.0-3.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/645684/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: arm64 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 (= 13), libhts-dev, libbz2-dev, libconst-fast-perl, libdevel-cover-perl, libfile-slurp-perl, libfile-which-perl, libipc-system-simple-perl, libjson-perl, libpod-coverage-perl, libtest-fatal-perl, libtry-tiny-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 ... 20082 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 (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libconst-fast-perl; however: Package libconst-fast-perl is not installed. pbuilder-satisfydepends-dummy depends on libdevel-cover-perl; however: Package libdevel-cover-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-slurp-perl; however: Package libfile-slurp-perl is not installed. pbuilder-satisfydepends-dummy depends on libfile-which-perl; however: Package libfile-which-perl is not installed. pbuilder-satisfydepends-dummy depends on libipc-system-simple-perl; however: Package libipc-system-simple-perl is not installed. pbuilder-satisfydepends-dummy depends on libjson-perl; however: Package libjson-perl is not installed. pbuilder-satisfydepends-dummy depends on libpod-coverage-perl; however: Package libpod-coverage-perl is not installed. pbuilder-satisfydepends-dummy depends on libtest-fatal-perl; however: Package libtest-fatal-perl is not installed. pbuilder-satisfydepends-dummy depends on libtry-tiny-perl; however: Package libtry-tiny-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} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libconst-fast-perl{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdata-optlist-perl{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdevel-cover-perl{a} libdevel-symdump-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libfile-slurp-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libipc-system-simple-perl{a} libjson-perl{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libparams-util-perl{a} libpipeline1{a} libpkgconf3{a} libpod-coverage-perl{a} libpod-parser-perl{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-install-perl{a} libtasn1-6-dev{a} libtest-fatal-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunbound8{a} liburi-perl{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libhttp-message-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc libtemplate-perl lynx publicsuffix wget 0 packages upgraded, 107 newly installed, 0 to remove and 0 not upgraded. Need to get 37.5 MB of archives. After unpacking 141 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-6 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-12 [91.4 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.2~rc1-2 [23.7 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 comerr-dev arm64 2.1-1.47.2~rc1-2 [55.7 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-8 [517 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 24 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.20 [915 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 35 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libparams-util-perl arm64 1.102-3+b1 [23.7 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 50 http://deb.debian.org/debian trixie/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get: 51 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libngtcp2-16 arm64 1.9.1-1 [109 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls8 arm64 1.9.1-1 [17.3 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.11.0-1 [331 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libldap-dev arm64 2.5.18+dfsg-3+b1 [300 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libnghttp3-dev arm64 1.6.0-2 [86.5 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.9.1-1 [23.0 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libngtcp2-dev arm64 1.9.1-1 [162 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.11.0-1 [459 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 liburi-perl all 5.30-1 [105 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libhtml-parser-perl arm64 3.83-1+b1 [97.5 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libdevel-cover-perl arm64 1.44-1+b1 [184 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libdevel-symdump-perl all 2.18-5 [15.8 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libfile-slurp-perl all 9999.32-2 [26.7 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libpod-parser-perl all 1.67-1 [94.1 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libpod-coverage-perl all 0.23-2 [22.1 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libtest-fatal-perl all 0.017-1 [13.2 kB] Fetched 37.5 MB in 0s (133 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20082 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. 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Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../015-libcom-err2_1.47.2~rc1-2_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2~rc1-2) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../016-comerr-dev_2.1-1.47.2~rc1-2_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.2~rc1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../017-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../018-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../019-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../020-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../021-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../022-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../023-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../024-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../025-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../026-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../027-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../028-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../029-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../030-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../031-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../032-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../033-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../034-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../035-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../036-libgssrpc4t64_1.21.3-3_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../037-libkadm5clnt-mit12_1.21.3-3_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../038-libkdb5-10t64_1.21.3-3_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../039-libkadm5srv-mit12_1.21.3-3_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-3) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../040-krb5-multidev_1.21.3-3_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-3) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../041-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../042-libbrotli-dev_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../043-libbz2-dev_1.0.8-6_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-6) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../044-libparams-util-perl_1.102-3+b1_arm64.deb ... Unpacking libparams-util-perl (1.102-3+b1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../045-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../046-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../047-libsub-exporter-perl_0.990-1_all.deb ... Unpacking libsub-exporter-perl (0.990-1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../048-libsub-exporter-progressive-perl_0.001013-3_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-3) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../049-libconst-fast-perl_0.014-2_all.deb ... Unpacking libconst-fast-perl (0.014-2) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../050-libsasl2-modules-db_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../051-libsasl2-2_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../052-libldap-2.5-0_2.5.18+dfsg-3+b1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../053-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../054-libnghttp3-9_1.6.0-2_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.6.0-2) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../055-libngtcp2-16_1.9.1-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.9.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../056-libngtcp2-crypto-gnutls8_1.9.1-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.9.1-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../057-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../058-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../059-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../060-libcurl3t64-gnutls_8.11.0-1_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.11.0-1) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../061-libevent-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:arm64. Preparing to unpack .../062-libunbound8_1.22.0-1_arm64.deb ... Unpacking libunbound8:arm64 (1.22.0-1) ... Selecting previously unselected package libgnutls-dane0t64:arm64. Preparing to unpack .../063-libgnutls-dane0t64_3.8.8-2_arm64.deb ... Unpacking libgnutls-dane0t64:arm64 (3.8.8-2) ... Selecting previously unselected package libgnutls-openssl27t64:arm64. Preparing to unpack .../064-libgnutls-openssl27t64_3.8.8-2_arm64.deb ... Unpacking libgnutls-openssl27t64:arm64 (3.8.8-2) ... Selecting previously unselected package libidn2-dev:arm64. Preparing to unpack .../065-libidn2-dev_2.3.7-2+b1_arm64.deb ... Unpacking libidn2-dev:arm64 (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit-dev:arm64. Preparing to unpack .../066-libp11-kit-dev_0.25.5-2+b1_arm64.deb ... Unpacking libp11-kit-dev:arm64 (0.25.5-2+b1) ... Selecting previously unselected package libtasn1-6-dev:arm64. Preparing to unpack .../067-libtasn1-6-dev_4.19.0-3+b3_arm64.deb ... Unpacking libtasn1-6-dev:arm64 (4.19.0-3+b3) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../068-libgmpxx4ldbl_2%3a6.3.0+dfsg-3_arm64.deb ... Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package libgmp-dev:arm64. Preparing to unpack .../069-libgmp-dev_2%3a6.3.0+dfsg-3_arm64.deb ... Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-3) ... Selecting previously unselected package nettle-dev:arm64. Preparing to unpack .../070-nettle-dev_3.10-1+b1_arm64.deb ... Unpacking nettle-dev:arm64 (3.10-1+b1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/allelecount-4.3.0/ && 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 > ../allelecount_4.3.0-3_source.changes dpkg-buildpackage: info: source package allelecount dpkg-buildpackage: info: source version 4.3.0-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0' dh_auto_clean --sourcedirectory=c cd c && make -j12 clean make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/c' rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log ./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/c' dh_auto_clean --sourcedirectory=perl make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0' dh_auto_configure --sourcedirectory=c dh_auto_configure --sourcedirectory=perl cd perl && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now" Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for alleleCount Writing MYMETA.yml and MYMETA.json make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0' dh_auto_build --sourcedirectory=c --no-parallel cd c && make -j1 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/c' rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log ./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno mkdir -p ./bin mkdir -p ./htslib_tmp #Do some magic to ensure we compile ALLELECOUNT with the static libhts.a rather than libhts.so ln -fs /libhts.a ./htslib_tmp/libhts.a gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -I/usr/local//include -Isrc/ -I/ -rdynamic -c src/bam_access.c -o src/bam_access.o gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -I/usr/local//include -Isrc/ -I/ -rdynamic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -o ./bin/alleleCounter ./src/bam_access.o -L./htslib_tmp -L/usr/local//lib -lhts -lpthread -lz -lbz2 -llzma -lm -ldl ./src/alleleCounter.c -Wl,-z,relro -Wl,-z,now gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -I/usr/local//include -Isrc/ -I/ -rdynamic ./src/bam_access.o -L./htslib_tmp -lhts -lpthread -lz -lbz2 -llzma -lm -ldl -L/usr/local//lib -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now tests/bam_access_tests.c -o tests/bam_access_tests tests/bam_access_tests.c: In function ‘test_bam_access_get_position_base_counts’: tests/bam_access_tests.c:45:13: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] 45 | int res = bam_access_get_position_base_counts(chr,pos,stats,0,NULL); | ^~~ sh ./tests/runtests.sh Running unit tests: ---- RUNNING: ./tests/bam_access_tests Performing pileup of 11250 reads at 1 198661939 ALL TESTS PASSED Tests run: 1 tests/bam_access_tests PASS remove tmp hts location rm -rf ./htslib_tmp Binaries have been compiled. make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/c' dh_auto_build --sourcedirectory=perl cd perl && make -j12 make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/perl' cp lib/Sanger/CGP/AlleleCount.pm blib/lib/Sanger/CGP/AlleleCount.pm cp lib/Sanger/CGP/AlleleCount/Genotype.pm blib/lib/Sanger/CGP/AlleleCount/Genotype.pm cp lib/Sanger/CGP/AlleleCount/ToJson.pm blib/lib/Sanger/CGP/AlleleCount/ToJson.pm cp bin/alleleCounter.pl blib/script/alleleCounter.pl cp bin/alleleCounterToJson.pl blib/script/alleleCounterToJson.pl "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/alleleCounter.pl "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/alleleCounterToJson.pl Manifying 2 pod documents Manifying 2 pod documents make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/perl' make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0' dh_auto_test --sourcedirectory=c cd c && make -j12 test make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/c' sh ./tests/runtests.sh Running unit tests: ---- RUNNING: ./tests/bam_access_tests Performing pileup of 11250 reads at 1 198661939 ALL TESTS PASSED Tests run: 1 tests/bam_access_tests PASS make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/c' dh_auto_test --sourcedirectory=perl cd perl && make -j12 test TEST_VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/perl' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/1_pm_compile.t .. ok 1 - use Sanger::CGP::AlleleCount; ok 2 - use Sanger::CGP::AlleleCount::ToJson; ok 3 - use Sanger::CGP::AlleleCount::Genotype; ok 4 - Check version inheritance exists (Sanger::CGP::AlleleCount) ok 5 - Check version inheritance exists (Sanger::CGP::AlleleCount::ToJson) ok 6 - An object of class 'Sanger::CGP::AlleleCount::ToJson' isa 'Sanger::CGP::AlleleCount::ToJson' ok 7 - Check version inheritance exists (Sanger::CGP::AlleleCount::Genotype) ok 8 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype' 1..8 ok t/2_pl_compile.t .. ok 1 - Compilation check: /build/reproducible-path/allelecount-4.3.0/perl/t/../bin/alleleCounterToJson.pl ok 2 - Compilation check: /build/reproducible-path/allelecount-4.3.0/perl/t/../bin/alleleCounter.pl 1..2 ok t/genotype.t ...... ok 1 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype' ok 2 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype' ok 3 - Check execution of loci profile (BAM) ok 4 - Expected result for defaults (BAM) ok 5 - Check execution of loci profile (BAM, pbq=20) ok 6 - Expected result for defaults (BAM, pbq=20) ok 7 - Check execution of loci profile (BAM, mapq=1) ok 8 - Expected result for defaults (BAM, mapq=1) ok 9 - Check execution of snp6 loci profile (BAM) ok 10 - Expected result for defaults (BAM) ok 11 - Check execution of snp6 loci profile (BAM, pbq=20) ok 12 - Expected result for defaults (BAM, pbq=20) ok 13 - Check execution of snp6 loci profile (BAM, mapq=1) ok 14 - Expected result for defaults (BAM, mapq>0) ok 15 - Check execution of loci profile (CRAM) ok 16 - Expected result for defaults (CRAM) ok 17 - Check execution of loci profile (CRAM, pbq=20) ok 18 - Expected result for defaults (CRAM, pbq=20) ok 19 - Check execution of loci profile (CRAM, mapq=1) ok 20 - Expected result for defaults (CRAM, mapq=1) ok 21 - Check execution of snp6 loci profile (CRAM) ok 22 - Expected result for defaults (CRAM) ok 23 - Check execution of snp6 loci profile (CRAM, pbq=20) ok 24 - Expected result for defaults (CRAM, pbq=20) ok 25 - Check execution of snp6 loci profile (CRAM, mapq=1) ok 26 - Expected result for defaults (CRAM, mapq=1) 1..26 ok t/tojson.t ........ ok 1 - An object of class 'Sanger::CGP::AlleleCount::ToJson' isa 'Sanger::CGP::AlleleCount::ToJson' ok 2 - Check conversion to JSON 1..2 ok All tests successful. Files=4, Tests=38, 1 wallclock secs ( 0.03 usr 0.02 sys + 0.76 cusr 0.20 csys = 1.01 CPU) Result: PASS make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/perl' make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0' dh_auto_install --sourcedirectory=c dh_auto_install --sourcedirectory=perl cd perl && make -j12 install DESTDIR=/build/reproducible-path/allelecount-4.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/perl' Manifying 2 pod documents Manifying 2 pod documents Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount.pm Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount/ToJson.pm Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount/Genotype.pm Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man1/alleleCounterToJson.pl.1p Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man1/alleleCounter.pl.1p Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::ToJson.3pm Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::Genotype.3pm Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounter.pl Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounterToJson.pl make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/perl' make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0' dh_install dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'allelecount' in '../allelecount_4.3.0-3_arm64.deb'. dpkg-deb: building package 'allelecount-dbgsym' in '../allelecount-dbgsym_4.3.0-3_arm64.deb'. dpkg-deb: building package 'liballelecount-perl' in '../liballelecount-perl_4.3.0-3_all.deb'. dpkg-genbuildinfo --build=binary -O../allelecount_4.3.0-3_arm64.buildinfo dpkg-genchanges --build=binary -O../allelecount_4.3.0-3_arm64.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/645684 and its subdirectories I: Current time: Thu Dec 12 17:09:34 -12 2024 I: pbuilder-time-stamp: 1734066574 Fri Dec 13 05:09:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Fri Dec 13 05:09:36 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Fri Dec 13 05:10:43 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Fri Dec 13 05:10:44 UTC 2024 I: allelecount_4.3.0-3_arm64.changes: Format: 1.8 Date: Tue, 10 Dec 2024 17:19:18 +0100 Source: allelecount Binary: allelecount allelecount-dbgsym liballelecount-perl Architecture: arm64 all Version: 4.3.0-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: allelecount - NGS copy number algorithms liballelecount-perl - Perl interface to NGS copy number algorithms Changes: allelecount (4.3.0-3) unstable; urgency=medium . * Build with make 4.4.1 (no-parallel) * Standards-Version: 4.7.0 (routine-update) * Update lintian override info format in d/liballelecount-perl.lintian-overrides on line 2. * Fix d/copyright (thanks to lrc) Checksums-Sha1: 885fe5d0e0d7304e674c3c15f2ec3c5644a19624 31808 allelecount-dbgsym_4.3.0-3_arm64.deb 8ae28a9837582a5d323b74d6c7d6779cdbc007ba 8032 allelecount_4.3.0-3_arm64.buildinfo 8cd8c2e3e4df3509d320d1e7424723f6c0d92479 29220 allelecount_4.3.0-3_arm64.deb cd04a75723f5739b74360ef0eae8d4d964b032fc 24948 liballelecount-perl_4.3.0-3_all.deb Checksums-Sha256: 772bb59eb6cf9ffbc9e9397da8db6a5536e397577b64f431a620cf782a116f1f 31808 allelecount-dbgsym_4.3.0-3_arm64.deb 255f00dbc83eaa9b4ed98744edaa6505529fb6902098a5897baabf77d32910d3 8032 allelecount_4.3.0-3_arm64.buildinfo df9252bb838fceedaf801e2a44d55e638ee5a5f0bfed31fbf5bcdfe9db093619 29220 allelecount_4.3.0-3_arm64.deb e336317bc15479a5206592f0606932f95bb05249f853d0b2888ee9efde9d75cc 24948 liballelecount-perl_4.3.0-3_all.deb Files: 9a6e0bc7abc611326ac4cf69f025ca6f 31808 debug optional allelecount-dbgsym_4.3.0-3_arm64.deb 3b1e4fe0648cae75c6920e92ca05b8d5 8032 science optional allelecount_4.3.0-3_arm64.buildinfo 8bd5242565623c4c1db45ae808e9eafc 29220 science optional allelecount_4.3.0-3_arm64.deb c3fa0c585879346f9e6be9aeb1a5a09f 24948 perl optional liballelecount-perl_4.3.0-3_all.deb Fri Dec 13 05:10:45 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_20-49155.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.yOy30I5m/allelecount_4.3.0-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.yOy30I5m/allelecount_4.3.0-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.yOy30I5m/allelecount_4.3.0-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.yOy30I5m/b1/allelecount_4.3.0-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.yOy30I5m/b2/allelecount_4.3.0-3_arm64.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: 0.332s) 0.332s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.016s) 0.016s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 635ms CPU time consumed: 630ms Fri Dec 13 05:10:46 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Fri Dec 13 05:10:46 UTC 2024 I: allelecount from trixie built successfully and reproducibly on arm64. Fri Dec 13 05:10:47 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Dec 13 05:10:47 UTC 2024 I: Submitting 12K b1/allelecount_4.3.0-3_arm64.buildinfo.asc Fri Dec 13 05:10:48 UTC 2024 I: Submitting 12K b2/allelecount_4.3.0-3_arm64.buildinfo.asc Fri Dec 13 05:10:48 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Dec 13 05:10:48 UTC 2024 I: Done submitting .buildinfo files. Fri Dec 13 05:10:48 UTC 2024 I: Removing signed allelecount_4.3.0-3_arm64.buildinfo.asc files: removed './b1/allelecount_4.3.0-3_arm64.buildinfo.asc' removed './b2/allelecount_4.3.0-3_arm64.buildinfo.asc'