Running as unit: rb-build-amd64_11-67732.service; invocation ID: 9737cb5eb99b44ad831fed136ec9af8e ==================================================================================== Tue Sep 16 14:26:59 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_11) on jenkins, called using "ionos1-amd64 ionos15-amd64" as arguments. Tue Sep 16 14:26:59 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-0latVZqB" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 16 14:26:59 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Tue Sep 16 14:26:59 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-lhB3hg' Tue Sep 16 14:27:00 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Tue Sep 16 14:27:00 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-MZPnqg' ok, let's check if smalt is building anywhere yet… ok, smalt is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of smalt in forky on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Tue Sep 16 14:27:15 UTC 2025 I: starting to build smalt/forky/amd64 on jenkins on '2025-09-16 14:26' Tue Sep 16 14:27:15 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_11/67732/console.log 1758032835 amd64 forky smalt Tue Sep 16 14:27:15 UTC 2025 I: Downloading source for forky/smalt=0.7.6-13 --2025-09-16 14:27:15-- 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% 248M=0s 2025-09-16 14:27:15 (248 MB/s) - ‘smalt_0.7.6-13.dsc’ saved [2100/2100] --2025-09-16 14:27:15-- 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% 248M=0s 2025-09-16 14:27:15 (248 MB/s) - ‘smalt_0.7.6-13.dsc’ saved [2100/2100] Tue Sep 16 14:27:15 UTC 2025 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----- Tue Sep 16 14:27:15 UTC 2025 I: Checking whether the package is not for us Tue Sep 16 14:27:15 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Tue Sep 16 14:27:15 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Tue Sep 16 14:27:15 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Tue Sep 16 14:27:15 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-pXpxaf' ==================================================================================== Tue Sep 16 14:27:16 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 smalt forky /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx 0.7.6-13" as arguments. Tue Sep 16 14:27:16 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-9Tn04SgQ" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 16 14:27:16 UTC 2025 I: Downloading source for forky/smalt=0.7.6-13 Reading package lists... NOTICE: 'smalt' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/smalt.git Please use: git clone https://salsa.debian.org/med-team/smalt.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 72.3 MB of source archives. Get:1 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (dsc) [2100 B] Get:2 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (tar) [72.3 MB] Get:3 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (diff) [9876 B] Fetched 72.3 MB in 1s (59.1 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'smalt' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/smalt.git Please use: git clone https://salsa.debian.org/med-team/smalt.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 72.3 MB of source archives. Get:1 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (dsc) [2100 B] Get:2 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (tar) [72.3 MB] Get:3 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (diff) [9876 B] Fetched 72.3 MB in 1s (59.1 MB/s) Download complete and in download only mode ============================================================================= Building smalt in forky on amd64 on ionos1-amd64 now. Date: Tue Sep 16 14:27:17 UTC 2025 Date UTC: Tue Sep 16 14:27:17 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 16 02:27:17 -12 2025 I: pbuilder-time-stamp: 1758032837 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 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/2276997/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='330d277fdc3b46f4aca498c798150282' 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='2276997' 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.rzXOzocx/pbuilderrc_ZoBd --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b1 --logfile b1/build.log smalt_0.7.6-13.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' 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 ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2276997/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: amd64 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 ... 19917 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} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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} python3.13{a} python3.13-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, 77 newly installed, 0 to remove and 0 not upgraded. Need to get 24.7 MB of archives. After unpacking 86.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 36 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libbambamc0 amd64 0.0.50-6+b2 [38.2 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 libbambamc-dev amd64 0.0.50-6+b2 [51.2 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 60 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libcurl3t64-gnutls amd64 8.15.0-1 [385 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 samtools amd64 1.22.1-1 [697 kB] Fetched 24.7 MB in 18s (1359 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../50-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../51-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../52-libnghttp3-9_1.11.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../53-libngtcp2-16_1.15.1-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.15.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../54-libngtcp2-crypto-gnutls8_1.15.1-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Selecting previously unselected package libpsl5t64:amd64. 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Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up libdeflate0:amd64 (1.23-2) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Sep 16 14:30:07 UTC 2025. Universal Time is now: Tue Sep 16 14:30:07 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up libncurses6:amd64 (6.5+20250216-2) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up libbambamc0:amd64 (0.0.50-6+b2) ... Setting up autopoint (0.23.1-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.11.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.15.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up readline-common (8.3-3) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up pkg-config:amd64 (1.8.1-4) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up python3.13 (3.13.7-1) ... Setting up libbambamc-dev:amd64 (0.0.50-6+b2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.7-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Setting up libcurl3t64-gnutls:amd64 (8.15.0-1) ... Setting up debhelper (13.26) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... Setting up samtools (1.22.1-1) ... Processing triggers for libc-bin (2.41-12) ... 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 amd64 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 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=x86_64-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/x86_64-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... yes checking emmintrin.h presence... yes checking for emmintrin.h... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-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 -j40 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c sequence.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -c -o libsgm_a-swsimd.o `test -f 'swsimd.c' || echo './'`swsimd.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -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 -fcf-protection -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.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 -fcf-protection -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.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 -fcf-protection -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.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 -fcf-protection -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.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; | ^ 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; | ^~~~~~ 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; | ^~~~~~ 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: | ^~~~ 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) | ~~~~~~~~~~^~~~~~~~ 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) | ~~~~~~~~~~^~~~~~~~ diffstr.c: In function 'diffStrGetDiffStats': 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) { | ^~ hashhit.c: In function 'hashCreateHitList': 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; | ^ 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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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"; | ^~~~~~~~~~~~~~~~~~~~~ smalt.c: In function 'cleanupSmaltOutput': smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function] 478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp) | ^~~~~~~~~~~~~ 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-swsimd.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -j40 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 -j40 check "TESTSUITEFLAGS=-j40 --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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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' /build/reproducible-path/smalt-0.7.6/test/formats.py:32: SyntaxWarning: invalid escape sequence '\d' CIGARSTR = compile("^cigar:([ABCDNRSP]):(\d{2})\s+(\S+)\s+(\d+)\s+(\d+)\s+([*+-])\s+" \ /build/reproducible-path/smalt-0.7.6/test/formats.py:33: SyntaxWarning: invalid escape sequence '\S' "(\S+)\s+(\d+)\s+(\d+)\s+\+\s+(\d+)\s+(.+)$") PASS: splitReads_test.py /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:13: SyntaxWarning: invalid escape sequence '\d' "Bbf^BcfBbdcfBdcfcddYbaB\dfYcc\ec_efeed\_cTebcacced"\ /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:14: SyntaxWarning: invalid escape sequence '\e' "bebf`^fa^cV`fde^\ecc`d`cbccfeTbdbeZcefccf^fccbfBc!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:20: SyntaxWarning: invalid escape sequence '\`' "edff^Yc^`dY`\\fefa^ddcYb^ef`adfdB\`f\`c`defce`adde!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:25: SyntaxWarning: invalid escape sequence '\B' "Yfffcc\BYBf`dedBeeaZf^c^adff`BbfeTB_bdf\`YfdeBfBdd"\ /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:26: SyntaxWarning: invalid escape sequence '\e' "eB_ae\eVff]dTedc_dcff^cVa_^d\\affdfdfddcadbbBT^fBd!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:32: SyntaxWarning: invalid escape sequence '\c' "B``bdZffbeMUcUaTfeceb`V^fecaddde\cfW^de[Bececec`B!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:37: SyntaxWarning: invalid escape sequence '\e' "daBZddeYdBfe`fBf`ecfdfcf`c\eacXdbLe^b``ccadK]e]^_T"\ /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:38: SyntaxWarning: invalid escape sequence '\T' "fccbcd\Tffb^Yfdfdf^efa\[fbfdad`X\\Ue_^eBfcfcfNfdf^!\n" 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 /build/reproducible-path/smalt-0.7.6/test/./xali_test.py:76: SyntaxWarning: invalid escape sequence '\S' REFNAMNO = compile("^\S+_(\d+)") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:5: SyntaxWarning: invalid escape sequence '\S' SAMSTR = re.compile("^(\S+)\t(\d+)\t(\S+)\t(\d+)\t(\d+)\t(\S+)\t(\S+)\t"\ /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:6: SyntaxWarning: invalid escape sequence '\d' "(\d+)\t([\+\-]*\d+)\t(\S+)\t(\S+)"\ /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:8: SyntaxWarning: invalid escape sequence '\S' TAGSTR = re.compile("^(\S{2}):([iZ]):(\S+)") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:13: SyntaxWarning: invalid escape sequence '\S' QNAMSTR = re.compile("^(\S+)\/([12])$") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:14: SyntaxWarning: invalid escape sequence '\d' ALISCOR = re.compile("\tAS:i:(\d+)") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:15: SyntaxWarning: invalid escape sequence '\d' CLIPSTART = re.compile("^(\d+)([HS])") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:16: SyntaxWarning: invalid escape sequence '\d' CLIPEND = re.compile("(\d+)([HS])$") 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 295743 new size 297868 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_amd64.deb'. dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-13_amd64.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_amd64.buildinfo dpkg-genchanges --build=binary -O../smalt_0.7.6-13_amd64.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/2276997 and its subdirectories I: Current time: Tue Sep 16 02:32:12 -12 2025 I: pbuilder-time-stamp: 1758033132 Tue Sep 16 14:32:12 UTC 2025 I: Signing ./b1/smalt_0.7.6-13_amd64.buildinfo as smalt_0.7.6-13_amd64.buildinfo.asc Tue Sep 16 14:32:12 UTC 2025 I: Signed ./b1/smalt_0.7.6-13_amd64.buildinfo as ./b1/smalt_0.7.6-13_amd64.buildinfo.asc Tue Sep 16 14:32:12 UTC 2025 - build #1 for smalt/forky/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Tue Sep 16 14:32:12 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-9Tn04SgQ, removing. /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 14:32 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 14:27 b2 -rw------- 1 jenkins jenkins 3185 Sep 16 14:27 rbuildlog.vA9tuJB -rw-rw-r-- 1 jenkins jenkins 2100 Jan 12 2024 smalt_0.7.6-13.dsc /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b1: total 70904 -rw-r--r-- 1 jenkins jenkins 73609 Sep 16 14:32 build.log -rw-r--r-- 1 jenkins jenkins 399280 Sep 16 14:32 smalt-dbgsym_0.7.6-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 71870676 Sep 16 14:32 smalt-examples_0.7.6-13_all.deb -rw-r--r-- 1 jenkins jenkins 9876 Sep 16 14:32 smalt_0.7.6-13.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2100 Sep 16 14:32 smalt_0.7.6-13.dsc -rw-r--r-- 1 jenkins jenkins 6622 Sep 16 14:32 smalt_0.7.6-13_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7504 Sep 16 14:32 smalt_0.7.6-13_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1726 Sep 16 14:32 smalt_0.7.6-13_amd64.changes -rw-r--r-- 1 jenkins jenkins 127500 Sep 16 14:32 smalt_0.7.6-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 1234 Sep 16 14:32 smalt_0.7.6-13_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b2: total 0 Tue Sep 16 14:32:13 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 16 02:27:17 -12 2025 I: pbuilder-time-stamp: 1758032837 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 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/2276997/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='330d277fdc3b46f4aca498c798150282' 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='2276997' 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.rzXOzocx/pbuilderrc_ZoBd --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b1 --logfile b1/build.log smalt_0.7.6-13.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' 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 ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2276997/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: amd64 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 ... 19917 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} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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} python3.13{a} python3.13-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, 77 newly installed, 0 to remove and 0 not upgraded. Need to get 24.7 MB of archives. After unpacking 86.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 36 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libbambamc0 amd64 0.0.50-6+b2 [38.2 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 libbambamc-dev amd64 0.0.50-6+b2 [51.2 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 60 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libcurl3t64-gnutls amd64 8.15.0-1 [385 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 samtools amd64 1.22.1-1 [697 kB] Fetched 24.7 MB in 18s (1359 kB/s) Preconfiguring packages ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up debhelper (13.26) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... Setting up samtools (1.22.1-1) ... Processing triggers for libc-bin (2.41-12) ... 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 amd64 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 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=x86_64-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/x86_64-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... yes checking emmintrin.h presence... yes checking for emmintrin.h... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-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 -j40 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c sequence.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -c -o libsgm_a-swsimd.o `test -f 'swsimd.c' || echo './'`swsimd.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -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 -fcf-protection -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.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 -fcf-protection -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.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 -fcf-protection -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.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 -fcf-protection -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.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; | ^ 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; | ^~~~~~ 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; | ^~~~~~ 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: | ^~~~ 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) | ~~~~~~~~~~^~~~~~~~ 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) | ~~~~~~~~~~^~~~~~~~ diffstr.c: In function 'diffStrGetDiffStats': 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) { | ^~ hashhit.c: In function 'hashCreateHitList': 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; | ^ 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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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"; | ^~~~~~~~~~~~~~~~~~~~~ smalt.c: In function 'cleanupSmaltOutput': smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function] 478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp) | ^~~~~~~~~~~~~ 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-swsimd.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -j40 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 -j40 check "TESTSUITEFLAGS=-j40 --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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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' /build/reproducible-path/smalt-0.7.6/test/formats.py:32: SyntaxWarning: invalid escape sequence '\d' CIGARSTR = compile("^cigar:([ABCDNRSP]):(\d{2})\s+(\S+)\s+(\d+)\s+(\d+)\s+([*+-])\s+" \ /build/reproducible-path/smalt-0.7.6/test/formats.py:33: SyntaxWarning: invalid escape sequence '\S' "(\S+)\s+(\d+)\s+(\d+)\s+\+\s+(\d+)\s+(.+)$") PASS: splitReads_test.py /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:13: SyntaxWarning: invalid escape sequence '\d' "Bbf^BcfBbdcfBdcfcddYbaB\dfYcc\ec_efeed\_cTebcacced"\ /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:14: SyntaxWarning: invalid escape sequence '\e' "bebf`^fa^cV`fde^\ecc`d`cbccfeTbdbeZcefccf^fccbfBc!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:20: SyntaxWarning: invalid escape sequence '\`' "edff^Yc^`dY`\\fefa^ddcYb^ef`adfdB\`f\`c`defce`adde!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:25: SyntaxWarning: invalid escape sequence '\B' "Yfffcc\BYBf`dedBeeaZf^c^adff`BbfeTB_bdf\`YfdeBfBdd"\ /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:26: SyntaxWarning: invalid escape sequence '\e' "eB_ae\eVff]dTedc_dcff^cVa_^d\\affdfdfddcadbbBT^fBd!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:32: SyntaxWarning: invalid escape sequence '\c' "B``bdZffbeMUcUaTfeceb`V^fecaddde\cfW^de[Bececec`B!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:37: SyntaxWarning: invalid escape sequence '\e' "daBZddeYdBfe`fBf`ecfdfcf`c\eacXdbLe^b``ccadK]e]^_T"\ /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:38: SyntaxWarning: invalid escape sequence '\T' "fccbcd\Tffb^Yfdfdf^efa\[fbfdad`X\\Ue_^eBfcfcfNfdf^!\n" 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 /build/reproducible-path/smalt-0.7.6/test/./xali_test.py:76: SyntaxWarning: invalid escape sequence '\S' REFNAMNO = compile("^\S+_(\d+)") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:5: SyntaxWarning: invalid escape sequence '\S' SAMSTR = re.compile("^(\S+)\t(\d+)\t(\S+)\t(\d+)\t(\d+)\t(\S+)\t(\S+)\t"\ /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:6: SyntaxWarning: invalid escape sequence '\d' "(\d+)\t([\+\-]*\d+)\t(\S+)\t(\S+)"\ /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:8: SyntaxWarning: invalid escape sequence '\S' TAGSTR = re.compile("^(\S{2}):([iZ]):(\S+)") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:13: SyntaxWarning: invalid escape sequence '\S' QNAMSTR = re.compile("^(\S+)\/([12])$") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:14: SyntaxWarning: invalid escape sequence '\d' ALISCOR = re.compile("\tAS:i:(\d+)") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:15: SyntaxWarning: invalid escape sequence '\d' CLIPSTART = re.compile("^(\d+)([HS])") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:16: SyntaxWarning: invalid escape sequence '\d' CLIPEND = re.compile("(\d+)([HS])$") 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 295743 new size 297868 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_amd64.deb'. dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-13_amd64.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_amd64.buildinfo dpkg-genchanges --build=binary -O../smalt_0.7.6-13_amd64.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/2276997 and its subdirectories I: Current time: Tue Sep 16 02:32:12 -12 2025 I: pbuilder-time-stamp: 1758033132 Tue Sep 16 14:32:13 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Tue Sep 16 14:32:13 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Tue Sep 16 14:32:13 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Tue Sep 16 14:32:13 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-P0OgNR' ==================================================================================== Mon Oct 19 20:55:14 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 smalt forky /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx 0.7.6-13" as arguments. Mon Oct 19 20:55:14 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-AjAEYem7" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Oct 19 20:55:14 UTC 2026 I: Downloading source for forky/smalt=0.7.6-13 Reading package lists... NOTICE: 'smalt' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/smalt.git Please use: git clone https://salsa.debian.org/med-team/smalt.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 72.3 MB of source archives. Get:1 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (dsc) [2100 B] Get:2 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (tar) [72.3 MB] Get:3 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (diff) [9876 B] Fetched 72.3 MB in 1s (58.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'smalt' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/smalt.git Please use: git clone https://salsa.debian.org/med-team/smalt.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 72.3 MB of source archives. Get:1 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (dsc) [2100 B] Get:2 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (tar) [72.3 MB] Get:3 http://deb.debian.org/debian forky/main smalt 0.7.6-13 (diff) [9876 B] Fetched 72.3 MB in 1s (58.4 MB/s) Download complete and in download only mode ============================================================================= Re-Building smalt in forky on amd64 on ionos15-amd64 now. Date: Mon Oct 19 20:55:15 UTC 2026 Date UTC: Mon Oct 19 20:55:15 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/pbuilderrc_ehSW + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' smalt = debian-installer -o smalt = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' smalt = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/pbuilderrc_ehSW --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b2 --logfile b2/build.log smalt_0.7.6-13.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 20 10:55:15 +14 2026 I: pbuilder-time-stamp: 1792443315 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 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/2228482/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 19 20:55 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2228482/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2228482/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=forky EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=897764a98e2f4ea996e052d5b3f31f22 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2228482 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/pbuilderrc_ehSW --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b2 --logfile b2/build.log smalt_0.7.6-13.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2228482/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: amd64 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 ... 19917 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} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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} python3.13{a} python3.13-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, 77 newly installed, 0 to remove and 0 not upgraded. Need to get 24.7 MB of archives. After unpacking 86.2 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 36 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libbambamc0 amd64 0.0.50-6+b2 [38.2 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 50 http://deb.debian.org/debian forky/main amd64 libbambamc-dev amd64 0.0.50-6+b2 [51.2 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.9-3 [1465 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 60 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.15.1-1 [140 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-gnutls8 amd64 1.15.1-1 [20.9 kB] Get: 69 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libcurl3t64-gnutls amd64 8.15.0-1 [385 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libdeflate0 amd64 1.23-2 [47.3 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 samtools amd64 1.22.1-1 [697 kB] Fetched 24.7 MB in 1s (16.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up python3.13-minimal (3.13.7-1) ... 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 ... 20251 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../50-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../51-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../52-libnghttp3-9_1.11.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.11.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../53-libngtcp2-16_1.15.1-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.15.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../54-libngtcp2-crypto-gnutls8_1.15.1-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Selecting previously unselected package libpsl5t64:amd64. 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Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.11.0-1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:amd64 (1.15.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up readline-common (8.3-3) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up pkg-config:amd64 (1.8.1-4) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libgnutls30t64:amd64 (3.8.9-3) ... Setting up python3.13 (3.13.7-1) ... Setting up libbambamc-dev:amd64 (0.0.50-6+b2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.7-1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.15.1-1) ... Setting up libcurl3t64-gnutls:amd64 (8.15.0-1) ... Setting up debhelper (13.26) ... Setting up libhts3t64:amd64 (1.22.1+ds2-1) ... Setting up samtools (1.22.1-1) ... Processing triggers for libc-bin (2.41-12) ... 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: user script /srv/workspace/pbuilder/2228482/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for forky I: user script /srv/workspace/pbuilder/2228482/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/smalt-0.7.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 amd64 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 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=x86_64-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/x86_64-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... yes checking emmintrin.h presence... yes checking for emmintrin.h... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-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 -j42 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c sequence.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -c -o libsgm_a-swsimd.o `test -f 'swsimd.c' || echo './'`swsimd.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -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 -fcf-protection -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.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 -fcf-protection -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.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 -fcf-protection -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.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 -fcf-protection -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c 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) | ~~~~~~~~~~^~~~~~~~ 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) | ~~~~~~~~~~^~~~~~~~ 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"; | ^~~~~~~~~~~~~~~~~~~~~ diffstr.c: In function 'diffStrGetDiffStats': 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) { | ^~ hashhit.c: In function 'hashCreateHitList': 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; | ^ smalt.c: In function 'cleanupSmaltOutput': smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ 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; | ^ 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; | ^~~~~~ 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; | ^~~~~~ 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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: | ^~~~ 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-swsimd.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -j42 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 -j42 check "TESTSUITEFLAGS=-j42 --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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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 -msse2 -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 -fcf-protection -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' /build/reproducible-path/smalt-0.7.6/test/formats.py:32: SyntaxWarning: invalid escape sequence '\d' CIGARSTR = compile("^cigar:([ABCDNRSP]):(\d{2})\s+(\S+)\s+(\d+)\s+(\d+)\s+([*+-])\s+" \ /build/reproducible-path/smalt-0.7.6/test/formats.py:33: SyntaxWarning: invalid escape sequence '\S' "(\S+)\s+(\d+)\s+(\d+)\s+\+\s+(\d+)\s+(.+)$") PASS: splitReads_test.py /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:13: SyntaxWarning: invalid escape sequence '\d' "Bbf^BcfBbdcfBdcfcddYbaB\dfYcc\ec_efeed\_cTebcacced"\ /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:14: SyntaxWarning: invalid escape sequence '\e' "bebf`^fa^cV`fde^\ecc`d`cbccfeTbdbeZcefccf^fccbfBc!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:20: SyntaxWarning: invalid escape sequence '\`' "edff^Yc^`dY`\\fefa^ddcYb^ef`adfdB\`f\`c`defce`adde!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:25: SyntaxWarning: invalid escape sequence '\B' "Yfffcc\BYBf`dedBeeaZf^c^adff`BbfeTB_bdf\`YfdeBfBdd"\ /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:26: SyntaxWarning: invalid escape sequence '\e' "eB_ae\eVff]dTedc_dcff^cVa_^d\\affdfdfddcadbbBT^fBd!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:32: SyntaxWarning: invalid escape sequence '\c' "B``bdZffbeMUcUaTfeceb`V^fecaddde\cfW^de[Bececec`B!\n", /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:37: SyntaxWarning: invalid escape sequence '\e' "daBZddeYdBfe`fBf`ecfdfcf`c\eacXdbLe^b``ccadK]e]^_T"\ /build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:38: SyntaxWarning: invalid escape sequence '\T' "fccbcd\Tffb^Yfdfdf^efa\[fbfdad`X\\Ue_^eBfcfcfNfdf^!\n" 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 /build/reproducible-path/smalt-0.7.6/test/./xali_test.py:76: SyntaxWarning: invalid escape sequence '\S' REFNAMNO = compile("^\S+_(\d+)") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:5: SyntaxWarning: invalid escape sequence '\S' SAMSTR = re.compile("^(\S+)\t(\d+)\t(\S+)\t(\d+)\t(\d+)\t(\S+)\t(\S+)\t"\ /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:6: SyntaxWarning: invalid escape sequence '\d' "(\d+)\t([\+\-]*\d+)\t(\S+)\t(\S+)"\ /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:8: SyntaxWarning: invalid escape sequence '\S' TAGSTR = re.compile("^(\S{2}):([iZ]):(\S+)") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:13: SyntaxWarning: invalid escape sequence '\S' QNAMSTR = re.compile("^(\S+)\/([12])$") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:14: SyntaxWarning: invalid escape sequence '\d' ALISCOR = re.compile("\tAS:i:(\d+)") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:15: SyntaxWarning: invalid escape sequence '\d' CLIPSTART = re.compile("^(\d+)([HS])") /build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:16: SyntaxWarning: invalid escape sequence '\d' CLIPEND = re.compile("(\d+)([HS])$") 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 295743 new size 297868 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_amd64.deb'. dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-13_amd64.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_amd64.buildinfo dpkg-genchanges --build=binary -O../smalt_0.7.6-13_amd64.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: user script /srv/workspace/pbuilder/2228482/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2228482/tmp/hooks/B01_cleanup finished 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/2228482 and its subdirectories I: Current time: Tue Oct 20 10:58:23 +14 2026 I: pbuilder-time-stamp: 1792443503 + false + set +x Mon Oct 19 20:58:23 UTC 2026 I: Signing ./b2/smalt_0.7.6-13_amd64.buildinfo as smalt_0.7.6-13_amd64.buildinfo.asc Mon Oct 19 20:58:23 UTC 2026 I: Signed ./b2/smalt_0.7.6-13_amd64.buildinfo as ./b2/smalt_0.7.6-13_amd64.buildinfo.asc Mon Oct 19 20:58:23 UTC 2026 - build #2 for smalt/forky/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Mon Oct 19 20:58:23 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-AjAEYem7, removing. /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx: total 92 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 14:32 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 14:35 b2 -rw------- 1 jenkins jenkins 77082 Sep 16 14:32 rbuildlog.vA9tuJB -rw-rw-r-- 1 jenkins jenkins 2100 Jan 12 2024 smalt_0.7.6-13.dsc /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b1: total 70908 -rw-r--r-- 1 jenkins jenkins 73609 Sep 16 14:32 build.log -rw-r--r-- 1 jenkins jenkins 399280 Sep 16 14:32 smalt-dbgsym_0.7.6-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 71870676 Sep 16 14:32 smalt-examples_0.7.6-13_all.deb -rw-r--r-- 1 jenkins jenkins 9876 Sep 16 14:32 smalt_0.7.6-13.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2100 Sep 16 14:32 smalt_0.7.6-13.dsc -rw-r--r-- 1 jenkins jenkins 6622 Sep 16 14:32 smalt_0.7.6-13_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7504 Sep 16 14:32 smalt_0.7.6-13_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1726 Sep 16 14:32 smalt_0.7.6-13_amd64.changes -rw-r--r-- 1 jenkins jenkins 127500 Sep 16 14:32 smalt_0.7.6-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 1234 Sep 16 14:32 smalt_0.7.6-13_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b2: total 70868 -rw-rw-r-- 1 jenkins jenkins 75536 Sep 16 14:35 build.log -rw-r--r-- 1 jenkins jenkins 399280 Sep 16 14:35 smalt-dbgsym_0.7.6-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 71870676 Sep 16 14:35 smalt-examples_0.7.6-13_all.deb -rw-r--r-- 1 jenkins jenkins 9876 Sep 16 14:35 smalt_0.7.6-13.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2100 Sep 16 14:35 smalt_0.7.6-13.dsc -rw-rw-r-- 1 jenkins jenkins 6622 Sep 16 14:35 smalt_0.7.6-13_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7504 Sep 16 14:35 smalt_0.7.6-13_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1726 Sep 16 14:35 smalt_0.7.6-13_amd64.changes -rw-r--r-- 1 jenkins jenkins 127500 Sep 16 14:35 smalt_0.7.6-13_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1234 Sep 16 14:35 smalt_0.7.6-13_source.changes Tue Sep 16 14:35:25 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Tue Sep 16 14:35:25 UTC 2025 I: smalt_0.7.6-13_amd64.changes: Format: 1.8 Date: Fri, 12 Jan 2024 07:00:11 +0100 Source: smalt Binary: smalt smalt-dbgsym smalt-examples Architecture: amd64 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: 97e92ad49bfd4a73e7ef6f690946dc9dbc13b739 399280 smalt-dbgsym_0.7.6-13_amd64.deb 3f39945f495a16d0ea4bf4c68082b3765665894a 71870676 smalt-examples_0.7.6-13_all.deb 7fe960a683516414853679e1614f26e50b8addc7 6622 smalt_0.7.6-13_amd64.buildinfo 4d13076d1645c0db9ec99b29561629a97c224f47 127500 smalt_0.7.6-13_amd64.deb Checksums-Sha256: 11036e20f9ea67f0a81de80c47dda416a8434f3537d6cced3b18e26fc81d7204 399280 smalt-dbgsym_0.7.6-13_amd64.deb ae8ee90c4e03e3f0a045bec1ac47375c9250e2c9917f19adcb01a8043d56e8d8 71870676 smalt-examples_0.7.6-13_all.deb 44b6550f66d99c11130c47af4b8ae3fd502d6797587702c27d699c00b5858621 6622 smalt_0.7.6-13_amd64.buildinfo 6314883455476b69299622b4158b9d17c6ef25c650e1629e2af516a3dd43fece 127500 smalt_0.7.6-13_amd64.deb Files: e86add568c7d68d4f52029376287348d 399280 debug optional smalt-dbgsym_0.7.6-13_amd64.deb 7a7a127e878d996d006d528924a2abc7 71870676 science optional smalt-examples_0.7.6-13_all.deb 3b235846d21c1a30bc53675761c4a798 6622 science optional smalt_0.7.6-13_amd64.buildinfo 22de2c144fdb04d43910589142d6d385 127500 science optional smalt_0.7.6-13_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/smalt_0.7.6-13.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/smalt_0.7.6-13.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/smalt_0.7.6-13.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/smalt_0.7.6-13.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/forky/amd64/smalt_0.7.6-13_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/smalt_0.7.6-13.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-16 14:32:13.118645250 +0000 +++ b2/build.log 2025-09-16 14:35:24.858875765 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 16 02:27:17 -12 2025 -I: pbuilder-time-stamp: 1758032837 +I: Current time: Tue Oct 20 10:55:15 +14 2026 +I: pbuilder-time-stamp: 1792443315 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -25,53 +25,85 @@ 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/2276997/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2228482/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 19 20:55 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2228482/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2228482/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='330d277fdc3b46f4aca498c798150282' - 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='2276997' - PS1='# ' - PS2='> ' + INVOCATION_ID=897764a98e2f4ea996e052d5b3f31f22 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2228482 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.rzXOzocx/pbuilderrc_ZoBd --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b1 --logfile b1/build.log smalt_0.7.6-13.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - 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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/pbuilderrc_ehSW --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b2 --logfile b2/build.log smalt_0.7.6-13.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2276997/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2228482/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -192,7 +224,7 @@ Get: 75 http://deb.debian.org/debian forky/main amd64 libhts3t64 amd64 1.22.1+ds2-1 [499 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libncurses6 amd64 6.5+20250216-2 [105 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 samtools amd64 1.22.1-1 [697 kB] -Fetched 24.7 MB in 18s (1359 kB/s) +Fetched 24.7 MB in 1s (16.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19917 files and directories currently installed.) @@ -459,8 +491,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Sep 16 14:30:07 UTC 2025. -Universal Time is now: Tue Sep 16 14:30:07 UTC 2025. +Local time is now: Mon Oct 19 20:56:20 UTC 2026. +Universal Time is now: Mon Oct 19 20:56:20 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -527,7 +559,11 @@ 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 +I: user script /srv/workspace/pbuilder/2228482/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2228482/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/smalt-0.7.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 @@ -641,7 +677,7 @@ debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6' dh_auto_build -a - make -j40 + make -j42 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' @@ -670,6 +706,41 @@ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c +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) + | ~~~~~~~~~~^~~~~~~~ +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) + | ~~~~~~~~~~^~~~~~~~ +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"; + | ^~~~~~~~~~~~~~~~~~~~~ +diffstr.c: In function 'diffStrGetDiffStats': +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) { + | ^~ +hashhit.c: In function 'hashCreateHitList': +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; + | ^ +smalt.c: In function 'cleanupSmaltOutput': +smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] + 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) + | ~~~~~~~~^~~~~~~ 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; ifmode, "r"); @@ -709,50 +789,6 @@ sequence.c:491:3: note: here 491 | case SEQIO_WRITE_GZIP_FASTA: | ^~~~ -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) - | ~~~~~~~~~~^~~~~~~~ -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) - | ~~~~~~~~~~^~~~~~~~ -diffstr.c: In function 'diffStrGetDiffStats': -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) { - | ^~ -hashhit.c: In function 'hashCreateHitList': -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; - | ^ -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, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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"; - | ^~~~~~~~~~~~~~~~~~~~~ -smalt.c: In function 'cleanupSmaltOutput': -smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter] - 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) - | ~~~~~~~~^~~~~~~ -alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function] - 478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp) - | ^~~~~~~~~~~~~ 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') @@ -787,12 +823,12 @@ ../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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -Wl,-z,relro -Wl,-z,now -o simqual simqual.o basqual.o diffstr.o ../src/libseq.a -lm -lz @@ -808,7 +844,7 @@ 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 -j40 + make -j42 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' @@ -831,7 +867,7 @@ 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 -j40 check "TESTSUITEFLAGS=-j40 --verbose" VERBOSE=1 + make -j42 check "TESTSUITEFLAGS=-j42 --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' @@ -961,12 +997,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2228482/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2228482/tmp/hooks/B01_cleanup finished 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/2276997 and its subdirectories -I: Current time: Tue Sep 16 02:32:12 -12 2025 -I: pbuilder-time-stamp: 1758033132 +I: removing directory /srv/workspace/pbuilder/2228482 and its subdirectories +I: Current time: Tue Oct 20 10:58:23 +14 2026 +I: pbuilder-time-stamp: 1792443503 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/smalt_0.7.6-13.diff: 76.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/smalt_0.7.6-13.diff.gz b2/build.log: 82.6% -- replaced with stdout Compressing the 1st log... b1/build.log: 83.1% -- replaced with stdout Tue Sep 16 14:35:28 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_smalt_forky_amd64_1758033328 + touch /var/log/reproducible-builds/diffoscope_stamp_smalt_forky_amd64_1758033328 + RESULT=0 + systemd-run '--description=diffoscope on smalt/0.7.6-13 in forky/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_11-67732 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx --run-session -c jenkins-reproducible-forky-diffoscope-560ea3de-d688-46bd-a902-c869af40065a -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/dbd-tmp-boQ7rGE ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/smalt_0.7.6-13.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/smalt_0.7.6-13.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/smalt_0.7.6-13.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b1/smalt_0.7.6-13_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b2/smalt_0.7.6-13_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_11-67732.service; invocation ID: b3579ea65dbb4b99ad38a5e257ba9bcb # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/smalt_0.7.6-13.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/smalt_0.7.6-13.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/smalt_0.7.6-13.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b1/smalt_0.7.6-13_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.rzXOzocx/b2/smalt_0.7.6-13_amd64.changes ## command (total time: 0.289s) 0.289s 1 call cmp (internal) ## has_same_content_as (total time: 0.290s) 0.290s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.292s) 0.292s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 517ms CPU time consumed: 172ms Memory peak: 17.9M (swap: 0B) _ _ ___ _ __ ___ __ _| | |_ / __| '_ ` _ \ / _` | | __| \__ \ | | | | | (_| | | |_ |___/_| |_| |_|\__,_|_|\__| Tue Sep 16 14:43:00 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Sep 16 14:43:00 UTC 2025 I: smalt from forky built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-16 14:43:01] INFO: Starting at 2025-09-16 14:43:01.116351 [2025-09-16 14:43:01] INFO: Generating the pages of 1 package(s) [2025-09-16 14:43:01] CRITICAL: https://tests.reproducible-builds.org/debian/forky/amd64/smalt didn't produce a buildlog, even though it has been built. [2025-09-16 14:43:01] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/smalt didn't produce a buildlog, even though it has been built. [2025-09-16 14:43:01] INFO: Finished at 2025-09-16 14:43:01.763706, took: 0:00:00.647361 Tue Sep 16 14:43:01 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/forky/amd64/smalt.html Tue Sep 16 14:43:01 UTC 2025 I: Removing signed smalt_0.7.6-13_amd64.buildinfo.asc files: removed './b1/smalt_0.7.6-13_amd64.buildinfo.asc' removed './b2/smalt_0.7.6-13_amd64.buildinfo.asc' 1758033781 amd64 forky smalt Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/smalt_0.7.6-13.rbuild.log: 80.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/smalt_0.7.6-13.rbuild.log.gz [2025-09-16 14:43:02] INFO: Starting at 2025-09-16 14:43:02.324690 [2025-09-16 14:43:02] INFO: Generating the pages of 1 package(s) [2025-09-16 14:43:02] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/smalt didn't produce a buildlog, even though it has been built. [2025-09-16 14:43:02] INFO: Finished at 2025-09-16 14:43:02.802596, took: 0:00:00.477911 All cleanup done. Tue Sep 16 14:43:03 UTC 2025 - total duration: 0h 16m 1s. Tue Sep 16 14:43:03 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-0latVZqB, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 16min 3.547s CPU time consumed: 5.321s Memory peak: 184.4M (swap: 0B)