Wed Dec 11 16:32:30 UTC 2024 I: starting to build allelecount/unstable/i386 on jenkins on '2024-12-11 16:32' Wed Dec 11 16:32:30 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_9/35579/console.log Wed Dec 11 16:32:30 UTC 2024 I: Downloading source for unstable/allelecount=4.3.0-3 --2024-12-11 16:32:30-- 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% 349M=0s 2024-12-11 16:32:30 (349 MB/s) - ‘allelecount_4.3.0-3.dsc’ saved [2409/2409] Wed Dec 11 16:32:30 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----- Wed Dec 11 16:32:30 UTC 2024 I: Checking whether the package is not for us Wed Dec 11 16:32:30 UTC 2024 I: Starting 1st build on remote node ionos2-i386.debian.net. Wed Dec 11 16:32:30 UTC 2024 I: Preparing to do remote build '1' on ionos2-i386.debian.net. Wed Dec 11 16:33:23 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 11 04:32:32 -12 2024 I: pbuilder-time-stamp: 1733934752 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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: using eatmydata during job 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/52633/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='ae02d55e4e6f406788911f50ce4503b0' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='52633' 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.uPSUE5e2/pbuilderrc_NobF --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.uPSUE5e2/b1 --logfile b1/build.log allelecount_4.3.0-3.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos2-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/52633/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: i386 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 ... 19952 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 38.7 MB of archives. After unpacking 131 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-6 [1198 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 comerr-dev i386 2.1-1.47.2~rc1-2 [55.9 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 24 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 debhelper all 13.20 [915 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 35 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libgssrpc4t64 i386 1.21.3-3 [63.1 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libkadm5clnt-mit12 i386 1.21.3-3 [43.2 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libkdb5-10t64 i386 1.21.3-3 [45.1 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libkadm5srv-mit12 i386 1.21.3-3 [57.0 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 krb5-multidev i386 1.21.3-3 [126 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 libbrotli-dev i386 1.1.0-2+b6 [313 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 libparams-util-perl i386 1.102-3+b1 [24.7 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 libsub-install-perl all 0.929-1 [10.5 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 50 http://deb.debian.org/debian unstable/main i386 libconst-fast-perl all 0.014-2 [8792 B] Get: 51 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.11.0-1 [403 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10+b1 [195 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libunbound8 i386 1.22.0-1 [632 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libgnutls-dane0t64 i386 3.8.8-2 [447 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libgnutls-openssl27t64 i386 3.8.8-2 [447 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libidn2-dev i386 2.3.7-2+b1 [126 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libp11-kit-dev i386 0.25.5-2+b1 [208 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libtasn1-6-dev i386 4.19.0-3+b3 [102 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-3 [329 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libgmp-dev i386 2:6.3.0+dfsg-3 [661 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 nettle-dev i386 3.10-1+b1 [1334 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libgnutls28-dev i386 3.8.8-2 [1453 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libkrb5-dev i386 1.21.3-3 [15.7 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 libldap-dev i386 2.5.18+dfsg-3+b1 [324 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libnghttp2-dev i386 1.64.0-1 [123 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 libnghttp3-dev i386 1.6.0-2 [101 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls-dev i386 1.9.1-1 [24.0 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libngtcp2-dev i386 1.9.1-1 [202 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 libpsl-dev i386 0.21.2-1.1+b1 [78.4 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 librtmp-dev i386 2.4+20151223.gitfa8646d.1-2+b5 [72.3 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libssl-dev i386 3.3.2-2 [2790 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 libssh2-1-dev i386 1.11.1-1 [407 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libzstd-dev i386 1.5.6+dfsg-1+b1 [355 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 libcurl4-gnutls-dev i386 8.11.0-1 [533 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.22-1 [48.1 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libdeflate-dev i386 1.22-1 [57.2 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 liburi-perl all 5.30-1 [105 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libhtml-parser-perl i386 3.83-1+b1 [101 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libdevel-cover-perl i386 1.44-1+b1 [186 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 libdevel-symdump-perl all 2.18-5 [15.8 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 libfile-slurp-perl all 9999.32-2 [26.7 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 libfile-which-perl all 1.27-2 [15.1 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 libhtscodecs2 i386 1.6.1-1 [70.8 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libhts3t64 i386 1.20+ds-2 [500 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 liblzma-dev i386 5.6.3-1+b1 [328 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libhts-dev i386 1.20+ds-2 [1693 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libpod-parser-perl all 1.67-1 [94.1 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libpod-coverage-perl all 0.23-2 [22.1 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libtry-tiny-perl all 0.32-1 [22.9 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libtest-fatal-perl all 0.017-1 [13.2 kB] Fetched 38.7 MB in 1s (48.5 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 ... 19952 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_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. 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Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../015-libcom-err2_1.47.2~rc1-2_i386.deb ... Unpacking libcom-err2:i386 (1.47.2~rc1-2) ... Selecting previously unselected package comerr-dev:i386. Preparing to unpack .../016-comerr-dev_2.1-1.47.2~rc1-2_i386.deb ... Unpacking comerr-dev:i386 (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:i386. Preparing to unpack .../023-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../024-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../025-libicu72_72.1-5+b1_i386.deb ... Unpacking libicu72:i386 (72.1-5+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../026-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../027-gettext_0.22.5-2_i386.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:i386. Preparing to unpack .../031-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../032-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../033-libkeyutils1_1.6.3-4_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../034-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../035-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ... Selecting previously unselected package libgssrpc4t64:i386. Preparing to unpack .../036-libgssrpc4t64_1.21.3-3_i386.deb ... Unpacking libgssrpc4t64:i386 (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:i386. Preparing to unpack .../037-libkadm5clnt-mit12_1.21.3-3_i386.deb ... Unpacking libkadm5clnt-mit12:i386 (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:i386. Preparing to unpack .../038-libkdb5-10t64_1.21.3-3_i386.deb ... Unpacking libkdb5-10t64:i386 (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:i386. Preparing to unpack .../039-libkadm5srv-mit12_1.21.3-3_i386.deb ... Unpacking libkadm5srv-mit12:i386 (1.21.3-3) ... Selecting previously unselected package krb5-multidev:i386. Preparing to unpack .../040-krb5-multidev_1.21.3-3_i386.deb ... Unpacking krb5-multidev:i386 (1.21.3-3) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../041-libbrotli1_1.1.0-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b6) ... Selecting previously unselected package libbrotli-dev:i386. Preparing to unpack .../042-libbrotli-dev_1.1.0-2+b6_i386.deb ... Unpacking libbrotli-dev:i386 (1.1.0-2+b6) ... Selecting previously unselected package libbz2-dev:i386. Preparing to unpack .../043-libbz2-dev_1.0.8-6_i386.deb ... Unpacking libbz2-dev:i386 (1.0.8-6) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../044-libparams-util-perl_1.102-3+b1_i386.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:i386. Preparing to unpack .../050-libsasl2-modules-db_2.1.28+dfsg1-8_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../051-libsasl2-2_2.1.28+dfsg1-8_i386.deb ... Unpacking libsasl2-2:i386 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:i386. Preparing to unpack .../052-libldap-2.5-0_2.5.18+dfsg-3+b1_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../053-libnghttp2-14_1.64.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:i386. Preparing to unpack .../054-libnghttp3-9_1.6.0-2_i386.deb ... Unpacking libnghttp3-9:i386 (1.6.0-2) ... Selecting previously unselected package libngtcp2-16:i386. Preparing to unpack .../055-libngtcp2-16_1.9.1-1_i386.deb ... Unpacking libngtcp2-16:i386 (1.9.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:i386. Preparing to unpack .../056-libngtcp2-crypto-gnutls8_1.9.1-1_i386.deb ... Unpacking libngtcp2-crypto-gnutls8:i386 (1.9.1-1) ... Selecting previously unselected package libpsl5t64:i386. Preparing to unpack .../057-libpsl5t64_0.21.2-1.1+b1_i386.deb ... Unpacking libpsl5t64:i386 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../058-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:i386. Preparing to unpack .../059-libssh2-1t64_1.11.1-1_i386.deb ... Unpacking libssh2-1t64:i386 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:i386. Preparing to unpack .../060-libcurl3t64-gnutls_8.11.0-1_i386.deb ... Unpacking libcurl3t64-gnutls:i386 (8.11.0-1) ... Selecting previously unselected package libevent-2.1-7t64:i386. Preparing to unpack .../061-libevent-2.1-7t64_2.1.12-stable-10+b1_i386.deb ... Unpacking libevent-2.1-7t64:i386 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:i386. Preparing to unpack .../062-libunbound8_1.22.0-1_i386.deb ... Unpacking libunbound8:i386 (1.22.0-1) ... Selecting previously unselected package libgnutls-dane0t64:i386. Preparing to unpack .../063-libgnutls-dane0t64_3.8.8-2_i386.deb ... Unpacking libgnutls-dane0t64:i386 (3.8.8-2) ... Selecting previously unselected package libgnutls-openssl27t64:i386. Preparing to unpack .../064-libgnutls-openssl27t64_3.8.8-2_i386.deb ... Unpacking libgnutls-openssl27t64:i386 (3.8.8-2) ... Selecting previously unselected package libidn2-dev:i386. Preparing to unpack .../065-libidn2-dev_2.3.7-2+b1_i386.deb ... Unpacking libidn2-dev:i386 (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit-dev:i386. Preparing to unpack .../066-libp11-kit-dev_0.25.5-2+b1_i386.deb ... Unpacking libp11-kit-dev:i386 (0.25.5-2+b1) ... Selecting previously unselected package libtasn1-6-dev:i386. Preparing to unpack .../067-libtasn1-6-dev_4.19.0-3+b3_i386.deb ... Unpacking libtasn1-6-dev:i386 (4.19.0-3+b3) ... Selecting previously unselected package libgmpxx4ldbl:i386. Preparing to unpack .../068-libgmpxx4ldbl_2%3a6.3.0+dfsg-3_i386.deb ... Unpacking libgmpxx4ldbl:i386 (2:6.3.0+dfsg-3) ... Selecting previously unselected package libgmp-dev:i386. Preparing to unpack .../069-libgmp-dev_2%3a6.3.0+dfsg-3_i386.deb ... Unpacking libgmp-dev:i386 (2:6.3.0+dfsg-3) ... Selecting previously unselected package nettle-dev:i386. Preparing to unpack .../070-nettle-dev_3.10-1+b1_i386.deb ... Unpacking nettle-dev:i386 (3.10-1+b1) ... Selecting previously unselected package libgnutls28-dev:i386. Preparing to unpack .../071-libgnutls28-dev_3.8.8-2_i386.deb ... Unpacking libgnutls28-dev:i386 (3.8.8-2) ... Selecting previously unselected package libkrb5-dev:i386. Preparing to unpack .../072-libkrb5-dev_1.21.3-3_i386.deb ... Unpacking libkrb5-dev:i386 (1.21.3-3) ... Selecting previously unselected package libldap-dev:i386. Preparing to unpack .../073-libldap-dev_2.5.18+dfsg-3+b1_i386.deb ... Unpacking libldap-dev:i386 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libpkgconf3:i386. Preparing to unpack .../074-libpkgconf3_1.8.1-4_i386.deb ... Unpacking libpkgconf3:i386 (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../075-pkgconf-bin_1.8.1-4_i386.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:i386. Preparing to unpack .../076-pkgconf_1.8.1-4_i386.deb ... Unpacking pkgconf:i386 (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:i386. Preparing to unpack .../077-libnghttp2-dev_1.64.0-1_i386.deb ... Unpacking libnghttp2-dev:i386 (1.64.0-1) ... Selecting previously unselected package libnghttp3-dev:i386. Preparing to unpack .../078-libnghttp3-dev_1.6.0-2_i386.deb ... Unpacking libnghttp3-dev:i386 (1.6.0-2) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:i386. Preparing to unpack .../079-libngtcp2-crypto-gnutls-dev_1.9.1-1_i386.deb ... Unpacking libngtcp2-crypto-gnutls-dev:i386 (1.9.1-1) ... Selecting previously unselected package libngtcp2-dev:i386. Preparing to unpack .../080-libngtcp2-dev_1.9.1-1_i386.deb ... Unpacking libngtcp2-dev:i386 (1.9.1-1) ... Selecting previously unselected package libpsl-dev:i386. Preparing to unpack .../081-libpsl-dev_0.21.2-1.1+b1_i386.deb ... Unpacking libpsl-dev:i386 (0.21.2-1.1+b1) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../082-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_i386.deb ... 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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 i386 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 -j11 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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -j11 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/ToJson.pm blib/lib/Sanger/CGP/AlleleCount/ToJson.pm cp lib/Sanger/CGP/AlleleCount/Genotype.pm blib/lib/Sanger/CGP/AlleleCount/Genotype.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 -j11 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 -j11 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/alleleCounter.pl ok 2 - Compilation check: /build/reproducible-path/allelecount-4.3.0/perl/t/../bin/alleleCounterToJson.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 ( 0.04 usr 0.00 sys + 1.02 cusr 0.12 csys = 1.18 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 -j11 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/alleleCounter.pl.1p 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/man3/Sanger::CGP::AlleleCount::Genotype.3pm 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/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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'allelecount' in '../allelecount_4.3.0-3_i386.deb'. dpkg-deb: building package 'liballelecount-perl' in '../liballelecount-perl_4.3.0-3_all.deb'. dpkg-deb: building package 'allelecount-dbgsym' in '../allelecount-dbgsym_4.3.0-3_i386.deb'. dpkg-genbuildinfo --build=binary -O../allelecount_4.3.0-3_i386.buildinfo dpkg-genchanges --build=binary -O../allelecount_4.3.0-3_i386.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/52633 and its subdirectories I: Current time: Wed Dec 11 04:33:22 -12 2024 I: pbuilder-time-stamp: 1733934802 Wed Dec 11 16:33:23 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom08-i386.debian.net. Wed Dec 11 16:33:23 UTC 2024 I: Preparing to do remote build '2' on infom08-i386.debian.net. Wed Dec 11 16:34:03 UTC 2024 I: Deleting $TMPDIR on infom08-i386.debian.net. Wed Dec 11 16:34:03 UTC 2024 I: allelecount_4.3.0-3_i386.changes: Format: 1.8 Date: Tue, 10 Dec 2024 17:19:18 +0100 Source: allelecount Binary: allelecount allelecount-dbgsym liballelecount-perl Architecture: i386 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: f7b48c6363fbd50465b1f30f5c3da79c2bb6fcf9 27884 allelecount-dbgsym_4.3.0-3_i386.deb 169eb26ea1249ceb3ebc5d151f4fb87b9883b1b8 7972 allelecount_4.3.0-3_i386.buildinfo 923690f1d3191f944bf708a49608194217b5a101 30644 allelecount_4.3.0-3_i386.deb cd04a75723f5739b74360ef0eae8d4d964b032fc 24948 liballelecount-perl_4.3.0-3_all.deb Checksums-Sha256: 339bc90de477b52a317c24ec3d3a5ac8e2e1aa233242205eed839518699500b0 27884 allelecount-dbgsym_4.3.0-3_i386.deb 5a4ba83bf6dc24e39f78621d24250a878d903353bef3569c7e5f3515c6b04ced 7972 allelecount_4.3.0-3_i386.buildinfo 9125eb9ba62a1dc6aa6d7858d0663468aeaeefa2784e3e5ae3a9e8e971055a6f 30644 allelecount_4.3.0-3_i386.deb e336317bc15479a5206592f0606932f95bb05249f853d0b2888ee9efde9d75cc 24948 liballelecount-perl_4.3.0-3_all.deb Files: 1e6e8700643cb42828f4efee12373d8c 27884 debug optional allelecount-dbgsym_4.3.0-3_i386.deb f185f37aa1cbfb301ab8fe531085b446 7972 science optional allelecount_4.3.0-3_i386.buildinfo df3f3f59d2ce8e935933d5697b740e17 30644 science optional allelecount_4.3.0-3_i386.deb c3fa0c585879346f9e6be9aeb1a5a09f 24948 perl optional liballelecount-perl_4.3.0-3_all.deb Wed Dec 11 16:34:04 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_9-35579.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.uPSUE5e2/allelecount_4.3.0-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.uPSUE5e2/allelecount_4.3.0-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.uPSUE5e2/allelecount_4.3.0-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.uPSUE5e2/b1/allelecount_4.3.0-3_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.uPSUE5e2/b2/allelecount_4.3.0-3_i386.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: 0.328s) 0.328s 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: 617ms CPU time consumed: 618ms Wed Dec 11 16:34:05 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Wed Dec 11 16:34:05 UTC 2024 I: allelecount from unstable built successfully and reproducibly on i386. Wed Dec 11 16:34:06 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Dec 11 16:34:06 UTC 2024 I: Submitting 12K b1/allelecount_4.3.0-3_i386.buildinfo.asc Wed Dec 11 16:34:07 UTC 2024 I: Submitting 12K b2/allelecount_4.3.0-3_i386.buildinfo.asc Wed Dec 11 16:34:08 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Dec 11 16:34:08 UTC 2024 I: Done submitting .buildinfo files. Wed Dec 11 16:34:08 UTC 2024 I: Removing signed allelecount_4.3.0-3_i386.buildinfo.asc files: removed './b1/allelecount_4.3.0-3_i386.buildinfo.asc' removed './b2/allelecount_4.3.0-3_i386.buildinfo.asc'