Thu May 9 23:36:56 UTC 2024 I: starting to build smalt/trixie/arm64 on jenkins on '2024-05-09 23:36' Thu May 9 23:36:56 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_14/40041/console.log Thu May 9 23:36:56 UTC 2024 I: Downloading source for trixie/smalt=0.7.6-13 --2024-05-09 23:36:56-- http://deb.debian.org/debian/pool/main/s/smalt/smalt_0.7.6-13.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2100 (2.1K) [text/prs.lines.tag] Saving to: ‘smalt_0.7.6-13.dsc’ 0K .. 100% 220M=0s 2024-05-09 23:36:56 (220 MB/s) - ‘smalt_0.7.6-13.dsc’ saved [2100/2100] Thu May 9 23:36:56 UTC 2024 I: smalt_0.7.6-13.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: smalt Binary: smalt, smalt-examples Architecture: any all Version: 0.7.6-13 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://www.sanger.ac.uk/science/tools/smalt-0 Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/smalt Vcs-Git: https://salsa.debian.org/med-team/smalt.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 13), zlib1g-dev, python3 , samtools, libbambamc-dev Package-List: smalt deb science optional arch=any smalt-examples deb science optional arch=all Checksums-Sha1: bfe5beaf8334b78ee7e98571c954a4b12d915895 72290533 smalt_0.7.6.orig.tar.gz 49e7d1d7918f2f4bb6689f8717439cce0ba63367 9876 smalt_0.7.6-13.debian.tar.xz Checksums-Sha256: 89ccdfe471edba3577b43de9ebfdaedb5cd6e26b02bf4000c554253433796b31 72290533 smalt_0.7.6.orig.tar.gz 9d3aa8baf497303066244cddd4e58848574caa277a66a0dd6afff08db262132a 9876 smalt_0.7.6-13.debian.tar.xz Files: c3215d70ba960c8fdc8e80191695c60b 72290533 smalt_0.7.6.orig.tar.gz 78eb75483d638a4c06329aba51225f1a 9876 smalt_0.7.6-13.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJCBAEBCgAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWg10sOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtHF9w/+NFR+AR4R+X2jLwjGWGtJOMlUZGK1LplihmyG MDEWfu1TlBmLZMjP5q7sizucDOS4ST1g76oVzH99lCEESjL7XuXgnicb0AYyLvsZ bpsEYfojo5gUpZTAZrGiKKWXQB8Axxb8GYN6YgPYcQVxDtzoM14eNM5tQbhUeaQk BNU/TQEkjD9VExZZ0CI7e79zg56eIi3N0Yd8/TRzalgES+CHkhv/YQHFpDexvv4s zXrB7eMub9AzFEZQZZ4SrMiWAXgwQ9KvxW8ZGl1KP8FED1yDqqj4d5CY9DfsZbS+ pAWHZjPbUe+XK/Gii8Wcq/X+X1F/MKa5Srv2vPS3mlKJJiJO9PdkE7CASbISWW40 GncENLdRJi+TxxjpT2lddxFmVQ+/JqrmFuWv+Hbvs/R+7yXZttoa5F0H3FVaLkCh 05W8FWywCQOo7V99C0awzJhjKD18JLoblXXbCb3pp67wPZZfF6nfX78JTorAJpTa zF0fnlsSSn9NJeAp0lbEphPsHDem0P1IHGBSfMgArg+W0nydNiuDGKYcIRMsZq8t FBgAXeDVm8POJ2OdRCBVOR2Oz86ECfq/qcmy7fsRahMej3QnfrN2ijWJ47MAw+7i a5r1KyyfW9MOh46izCF1uIfb8tlkObJewP00RneQDiS1cM20zTzC9fcHufa/B15r M2pBT1E= =HB0A -----END PGP SIGNATURE----- Thu May 9 23:36:56 UTC 2024 I: Checking whether the package is not for us Thu May 9 23:36:56 UTC 2024 I: Starting 1st build on remote node codethink01-arm64.debian.net. Thu May 9 23:36:56 UTC 2024 I: Preparing to do remote build '1' on codethink01-arm64.debian.net. Thu May 9 23:41:25 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 11 17:59:59 -12 2025 I: pbuilder-time-stamp: 1749707999 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 [smalt_0.7.6-13.dsc] I: copying [./smalt_0.7.6.orig.tar.gz] I: copying [./smalt_0.7.6-13.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jan 12 06:08:11 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./smalt_0.7.6-13.dsc: no acceptable signature found dpkg-source: info: extracting smalt in smalt-0.7.6 dpkg-source: info: unpacking smalt_0.7.6.orig.tar.gz dpkg-source: info: unpacking smalt_0.7.6-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 2to3.patch dpkg-source: info: applying add-runstatedir.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2126730/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='924550ce6209449c84dca2a15886de59' 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='2126730' 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.Rark3Zhs/pbuilderrc_MeP5 --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.Rark3Zhs/b1 --logfile b1/build.log smalt_0.7.6-13.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 codethink01-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 10 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2126730/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), zlib1g-dev, python3, samtools, libbambamc-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19744 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on libbambamc-dev; however: Package libbambamc-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbambamc-dev{a} libbambamc0{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 70 newly installed, 0 to remove and 0 not upgraded. Need to get 28.6 MB of archives. After unpacking 114 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 36 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libbambamc0 arm64 0.0.50-6+b1 [34.6 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libbambamc-dev arm64 0.0.50-6+b1 [48.0 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 56 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.19+ds-1.1+b1 [413 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libncurses6 arm64 6.4+20240414-1 [95.6 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 samtools arm64 1.19.2-1+b1 [617 kB] Fetched 28.6 MB in 0s (132 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19744 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_arm64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:arm64 (3.11.9-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20060 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_arm64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../5-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21052 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../23-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../25-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-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 .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libbambamc0:arm64. Preparing to unpack .../31-libbambamc0_0.0.50-6+b1_arm64.deb ... Unpacking libbambamc0:arm64 (0.0.50-6+b1) ... Selecting previously unselected package libpkgconf3:arm64. Preparing to unpack .../32-libpkgconf3_1.8.1-1+b2_arm64.deb ... Unpacking libpkgconf3:arm64 (1.8.1-1+b2) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../33-pkgconf-bin_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../34-pkgconf_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-1+b2) ... Selecting previously unselected package pkg-config:arm64. Preparing to unpack .../35-pkg-config_1.8.1-1+b2_arm64.deb ... Unpacking pkg-config:arm64 (1.8.1-1+b2) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../36-zlib1g-dev_1%3a1.3.dfsg-3.1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Selecting previously unselected package libbambamc-dev:arm64. Preparing to unpack .../37-libbambamc-dev_0.0.50-6+b1_arm64.deb ... Unpacking libbambamc-dev:arm64 (0.0.50-6+b1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../38-libbrotli1_1.1.0-2+b3_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../39-libcom-err2_1.47.1~rc2-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1~rc2-1) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../40-libkrb5support0_1.20.1-6+b1_arm64.deb ... Unpacking libkrb5support0:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../41-libk5crypto3_1.20.1-6+b1_arm64.deb ... Unpacking libk5crypto3:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../42-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../43-libkrb5-3_1.20.1-6+b1_arm64.deb ... Unpacking libkrb5-3:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../44-libgssapi-krb5-2_1.20.1-6+b1_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../45-libsasl2-modules-db_2.1.28+dfsg1-6_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../46-libsasl2-2_2.1.28+dfsg1-6_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../47-libldap-2.5-0_2.5.17+dfsg-1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../48-libnghttp2-14_1.61.0-1+b1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../49-libpsl5t64_0.21.2-1.1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../50-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../51-libssh2-1t64_1.11.0-4.1+b2_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../52-libcurl3t64-gnutls_8.7.1-3_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.7.1-3) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../53-libdeflate0_1.20-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.20-1) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../54-libhtscodecs2_1.6.0-1+b1_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.0-1+b1) ... Selecting previously unselected package libhts3t64:arm64. Preparing to unpack .../55-libhts3t64_1.19+ds-1.1+b1_arm64.deb ... Unpacking libhts3t64:arm64 (1.19+ds-1.1+b1) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../56-libncurses6_6.4+20240414-1_arm64.deb ... Unpacking libncurses6:arm64 (6.4+20240414-1) ... Selecting previously unselected package samtools. Preparing to unpack .../57-samtools_1.19.2-1+b1_arm64.deb ... Unpacking samtools (1.19.2-1+b1) ... Setting up libhtscodecs2:arm64 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.61.0-1+b1) ... Setting up libdeflate0:arm64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:arm64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up libkrb5support0:arm64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Jun 12 06:00:17 UTC 2025. Universal Time is now: Thu Jun 12 06:00:17 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:arm64 (1.8.1-1+b2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libncurses6:arm64 (6.4+20240414-1) ... Setting up libbambamc0:arm64 (0.0.50-6+b1) ... Setting up autopoint (0.21-14) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:arm64 (1.20.1-6+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:arm64 (1.20.1-6+b1) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Setting up pkgconf:arm64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up pkg-config:arm64 (1.8.1-1+b2) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up libbambamc-dev:arm64 (0.0.50-6+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-3) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3t64:arm64 (1.19+ds-1.1+b1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up samtools (1.19.2-1+b1) ... Processing triggers for libc-bin (2.38-7) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/smalt-0.7.6/ && 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 > ../smalt_0.7.6-13_source.changes dpkg-buildpackage: info: source package smalt dpkg-buildpackage: info: source version 0.7.6-13 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/smalt-0.7.6' dh_auto_clean rm -rf test/*.pyc misc/*.pyc test/tmp find . -type d -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' dh_clean debian/rules binary dh binary dh_update_autotools_config cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead debian/rules override_dh_autoreconf make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' echo "Do nothing - fails because auf broken upstream autoconf stuff" Do nothing - fails because auf broken upstream autoconf stuff make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' dh_auto_configure -- CONFIG_SHELL=/bin/bash ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking CONFIG_SHELL=/bin/bash checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for icc... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... none checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for ranlib... ranlib checking for a Python interpreter with version >= 2.6... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.1 checking for python3 platform... linux checking for python3 script directory... ${prefix}/lib/python3.1/site-packages checking for python3 extension module directory... ${exec_prefix}/lib/python3.1/site-packages checking for samtools... yes checking for sam_open in -lbam... no checking for BAMBAMC... yes checking for gzread in -lz... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking pthread.h usability... yes checking pthread.h presence... yes checking for pthread.h... yes checking semaphore.h usability... yes checking semaphore.h presence... yes checking for semaphore.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking emmintrin.h usability... no checking emmintrin.h presence... no checking for emmintrin.h... no checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating test/data/Makefile config.status: creating misc/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' dh_auto_build -a make -j12 make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6' make all-recursive make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6' Making all in src make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c elib.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c filio.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c sequence.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsgm_a-score.o `test -f 'score.c' || echo './'`score.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsgm_a-diffstr.o `test -f 'diffstr.c' || echo './'`diffstr.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsgm_a-alibuffer.o `test -f 'alibuffer.c' || echo './'`alibuffer.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsgm_a-alignment.o `test -f 'alignment.c' || echo './'`alignment.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c sequence.c: In function 'make3BitMangledCodec': sequence.c:298:14: warning: comparison of integer expressions of different signedness: 'int' and 'enum SEQ_CONSTANTS' [-Wsign-compare] 298 | for (i=1; iOUTBUFSIZE) linewidth = OUTBUFSIZE; | ^ hashhit.c:1559:18: warning: comparison of integer expressions of different signedness: 'int' and 'enum ' [-Wsign-compare] 1559 | if (maxnhits < HITLST_MINSIZ) maxnhits = HITLST_MINSIZ; | ^ hashidx.c: In function 'countPerfectKey': hashidx.c:191:77: warning: unused parameter 'tuplectr' [-Wunused-parameter] 191 | static int countPerfectKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ hashidx.c: In function 'countCollisionKey': hashidx.c:206:79: warning: unused parameter 'tuplectr' [-Wunused-parameter] 206 | static int countCollisionKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ hashidx.c: In function 'collectWords': hashidx.c:223:74: warning: unused parameter 'tuplectr' [-Wunused-parameter] 223 | static int collectWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c hashidx.c: In function 'countWords': hashidx.c:265:72: warning: unused parameter 'tuplectr' [-Wunused-parameter] 265 | static int countWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ sequence.c: In function 'seqFastqGetConstSequence': sequence.c:2079:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2079 | if (length) | ^~ sequence.c:2081:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2081 | return NULL; | ^~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c sequence.c: In function 'seqFastqGetSequence': sequence.c:2094:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2094 | if (length) | ^~ sequence.c:2096:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2096 | return NULL; | ^~~~~~ hashidx.c: At top level: hashidx.c:446:18: warning: 'getWordHisto' defined but not used [-Wunused-function] 446 | static WORDNUM_t getWordHisto(WORDNUM_t *counts, HASHNUM_t n, const HashTable *htp) | ^~~~~~~~~~~~ hashidx.c:63:19: warning: 'HASHTABFIL_READERRMSG' defined but not used [-Wunused-const-variable=] 63 | static const char HASHTABFIL_READERRMSG[] = "when reading hash table file"; | ^~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c sequence.c: In function 'seqIOopen': sequence.c:489:5: warning: this statement may fall through [-Wimplicit-fallthrough=] 489 | strcpy(p->fmode, "r"); | ^~~~~~~~~~~~~~~~~~~~~ sequence.c:491:3: note: here 491 | case SEQIO_WRITE_GZIP_FASTA: | ^~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c segment.c:1375:12: warning: 'checkCANDARRsequential' defined but not used [-Wunused-function] 1375 | static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs) | ^~~~~~~~~~~~~~~~~~~~~~ segment.c:1330:13: warning: 'labelSEGCANDWithinInsertRange' defined but not used [-Wunused-function] 1330 | static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ smalt.c: In function 'cleanupSmaltOutput': smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c rm -f libseq.a ar cru libseq.a elib.o filio.o sequence.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseq.a rm -f libsgm.a ar cru libsgm.a libsgm_a-score.o libsgm_a-diffstr.o libsgm_a-alibuffer.o libsgm_a-alignment.o libsgm_a-sort.o libsgm_a-array.o libsgm_a-interval.o libsgm_a-hashidx.o libsgm_a-hashhit.o libsgm_a-segment.o libseq.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libsgm.a gcc -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o smalt smalt-smalt.o smalt-menu.o smalt-threads.o smalt-infmt.o smalt-results.o smalt-resultpairs.o smalt-report.o smalt-rmap.o smalt-insert.o libsgm.a libseq.a -lbambamc -lz -lm -lpthread -lz make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/src' Making all in test make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make[5]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make[5]: Nothing to be done for 'all-am'. make[5]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' Making all in misc make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/misc' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c simread.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c rsample.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c fetchseq.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c splitreads.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c mixreads.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c splitmates.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c readstats.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c trunkreads.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c basqcol.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c basqual.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c simqual.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c ../src/diffstr.c: In function 'diffStrGetDiffStats': ../src/diffstr.c:978:22: warning: the comparison will always evaluate as 'true' for the pointer operand in 'diffstrp + 1' must not be NULL [-Waddress] 978 | if (diffstrp+1 != NULL) { | ^~ gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o trunkreads trunkreads.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o readstats readstats.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o splitreads splitreads.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o splitmates splitmates.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o fetchseq fetchseq.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o mixreads mixreads.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o basqcol basqcol.o basqual.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o simread simread.o rsample.o ../src/libsgm.a ../src/libseq.a -lm -lz gcc -I../src/ -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o simqual simqual.o basqual.o diffstr.o ../src/libseq.a -lm -lz make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/misc' make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6' make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make -C test sequenceReverseComplement_test make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c sequenceReverseComplement_test.c gcc -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o sequenceReverseComplement_test sequenceReverseComplement_test.o ../src/libseq.a -lz make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' dh_auto_build -Nsmalt make -j12 make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' make all-recursive make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6' Making all in src make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/src' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/src' Making all in test make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' Making all in misc make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/misc' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/misc' make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6' make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' Making check in src make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/src' Making check in test make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make sequenceReverseComplement_test smalt_Xali_test make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' make[4]: 'sequenceReverseComplement_test' is up to date. gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt_Xali_test-smalt.o `test -f '../src/smalt.c' || echo './'`../src/smalt.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt_Xali_test-menu.o `test -f '../src/menu.c' || echo './'`../src/menu.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt_Xali_test-threads.o `test -f '../src/threads.c' || echo './'`../src/threads.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt_Xali_test-infmt.o `test -f '../src/infmt.c' || echo './'`../src/infmt.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt_Xali_test-results.o `test -f '../src/results.c' || echo './'`../src/results.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt_Xali_test-resultpairs.o `test -f '../src/resultpairs.c' || echo './'`../src/resultpairs.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt_Xali_test-insert.o `test -f '../src/insert.c' || echo './'`../src/insert.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt_Xali_test-report.o `test -f '../src/report.c' || echo './'`../src/report.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.c ../src/smalt.c: In function 'cleanupSmaltOutput': ../src/smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ gcc -I../src/ -I../test -Wall -Wextra -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wl,-z,relro -Wl,-z,now -o smalt_Xali_test smalt_Xali_test-smalt.o smalt_Xali_test-menu.o smalt_Xali_test-threads.o smalt_Xali_test-infmt.o smalt_Xali_test-results.o smalt_Xali_test-resultpairs.o smalt_Xali_test-insert.o smalt_Xali_test-report.o smalt_Xali_test-rmap.o ../src/libsgm.a ../src/libseq.a -lbambamc -lz -lm -lpthread -lz make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' make check-TESTS make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test' PASS: splitReads_test.py PASS: results_split_test.py PASS: ouform_cigar_test.py PASS: sample_test.py PASS: cigar_test.py PASS: mthread_test.py PASS: ioform_test.py PASS: xali_test.py PASS: bam_cigar_test.py ================== All 9 tests passed ================== make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test' Making check in misc make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/misc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/misc' make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6' make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6' make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' # upstream install does install more files than needed make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' dh_install # fix path to smalt executable in examples for py in `ls test/*.py` ; do \ sed 's#PROGNAM = "../src/smalt"#PROGNAM = "/usr/bin/smalt"#' ${py} > debian/smalt-examples/usr/share/doc/smalt/${py} ; \ done make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6' dh_install -Nsmalt-examples dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/smalt/usr/bin/smalt: DWARF compression not beneficial - old size 290406 new size 293126 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'smalt' in '../smalt_0.7.6-13_arm64.deb'. dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-13_arm64.deb'. dpkg-deb: building package 'smalt-examples' in '../smalt-examples_0.7.6-13_all.deb'. dpkg-genbuildinfo --build=binary -O../smalt_0.7.6-13_arm64.buildinfo dpkg-genchanges --build=binary -O../smalt_0.7.6-13_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/2126730 and its subdirectories I: Current time: Wed Jun 11 18:04:15 -12 2025 I: pbuilder-time-stamp: 1749708255 Thu May 9 23:41:26 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Thu May 9 23:41:26 UTC 2024 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Thu May 9 23:45:48 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Thu May 9 23:45:49 UTC 2024 I: smalt_0.7.6-13_arm64.changes: Format: 1.8 Date: Fri, 12 Jan 2024 07:00:11 +0100 Source: smalt Binary: smalt smalt-dbgsym smalt-examples Architecture: arm64 all Version: 0.7.6-13 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: smalt - Sequence Mapping and Alignment Tool smalt-examples - Sequence Mapping and Alignment Tool (examples) Closes: 1047681 Changes: smalt (0.7.6-13) unstable; urgency=medium . * Fix clean target Closes: #1047681 * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 338b425268037cb68e3f308f2bc5fd2c7127c671 387908 smalt-dbgsym_0.7.6-13_arm64.deb 3f39945f495a16d0ea4bf4c68082b3765665894a 71870676 smalt-examples_0.7.6-13_all.deb 3ba56e3e154648d9b863b2a5407bbf3fbfbf4f01 6815 smalt_0.7.6-13_arm64.buildinfo 067acaf6613348f2894f2d023ccbca1dfe84cb05 104616 smalt_0.7.6-13_arm64.deb Checksums-Sha256: fc8fbe91ce7883bb5b4c247ebd2f0999528bcacc8425571215e2551ebf4abd09 387908 smalt-dbgsym_0.7.6-13_arm64.deb ae8ee90c4e03e3f0a045bec1ac47375c9250e2c9917f19adcb01a8043d56e8d8 71870676 smalt-examples_0.7.6-13_all.deb f5d166da4d0b3674d09e795bb0f27a082e2dcda037728aa035f0ee45d94eef39 6815 smalt_0.7.6-13_arm64.buildinfo 5201ae8f1167068c2aa599d92fd9ad68f7f39a67092040953c3d5cb96999eb34 104616 smalt_0.7.6-13_arm64.deb Files: 49fc6ce3e4d2447ea5de1289b1702a19 387908 debug optional smalt-dbgsym_0.7.6-13_arm64.deb 7a7a127e878d996d006d528924a2abc7 71870676 science optional smalt-examples_0.7.6-13_all.deb e3e42af5ccbc27f727fe8c70c167309a 6815 science optional smalt_0.7.6-13_arm64.buildinfo a63f4aa7cfd78016c0466fb030ec5f27 104616 science optional smalt_0.7.6-13_arm64.deb Thu May 9 23:45:50 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_14-40041.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Rark3Zhs/smalt_0.7.6-13.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Rark3Zhs/smalt_0.7.6-13.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Rark3Zhs/smalt_0.7.6-13.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Rark3Zhs/b1/smalt_0.7.6-13_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Rark3Zhs/b2/smalt_0.7.6-13_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: 1.147s) 1.147s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.785s) 0.785s 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: 1.494s CPU time consumed: 1.494s Thu May 9 23:45:52 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Thu May 9 23:45:52 UTC 2024 I: smalt from trixie built successfully and reproducibly on arm64. Thu May 9 23:45:54 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 9 23:45:54 UTC 2024 I: Submitting 8.0K b1/smalt_0.7.6-13_arm64.buildinfo.asc Thu May 9 23:45:55 UTC 2024 I: Submitting 8.0K b2/smalt_0.7.6-13_arm64.buildinfo.asc Thu May 9 23:45:56 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 9 23:45:56 UTC 2024 I: Done submitting .buildinfo files. Thu May 9 23:45:56 UTC 2024 I: Removing signed smalt_0.7.6-13_arm64.buildinfo.asc files: removed './b1/smalt_0.7.6-13_arm64.buildinfo.asc' removed './b2/smalt_0.7.6-13_arm64.buildinfo.asc'