Running as unit: rb-build-arm64_10-46016.service ==================================================================================== Sun Nov 24 15:37:54 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_10) on jenkins, called using "codethink04-arm64 codethink02-arm64" as arguments. Sun Nov 24 15:37:54 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Qm5vKXRX" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Nov 24 15:37:54 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sun Nov 24 15:37:54 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-jnGco6' Sun Nov 24 15:37:54 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Sun Nov 24 15:37:54 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-tedpLI' ok, let's check if sumaclust is building anywhere yet… ok, sumaclust is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of sumaclust in unstable on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink02-arm64.debian.net. ============================================================================= Sun Nov 24 15:38:11 UTC 2024 I: starting to build sumaclust/unstable/arm64 on jenkins on '2024-11-24 15:37' Sun Nov 24 15:38:11 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/46016/console.log 1732462692 arm64 unstable sumaclust Sun Nov 24 15:38:12 UTC 2024 I: Downloading source for unstable/sumaclust=1.0.36+ds-2 --2024-11-24 15:38:12-- http://deb.debian.org/debian/pool/main/s/sumaclust/sumaclust_1.0.36%2bds-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2050 (2.0K) [text/prs.lines.tag] Saving to: ‘sumaclust_1.0.36+ds-2.dsc’ 0K .. 100% 308M=0s 2024-11-24 15:38:12 (308 MB/s) - ‘sumaclust_1.0.36+ds-2.dsc’ saved [2050/2050] --2024-11-24 15:38:12-- http://deb.debian.org/debian/pool/main/s/sumaclust/sumaclust_1.0.36%2bds-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2050 (2.0K) [text/prs.lines.tag] Saving to: ‘sumaclust_1.0.36+ds-2.dsc’ 0K .. 100% 308M=0s 2024-11-24 15:38:12 (308 MB/s) - ‘sumaclust_1.0.36+ds-2.dsc’ saved [2050/2050] Sun Nov 24 15:38:12 UTC 2024 I: sumaclust_1.0.36+ds-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sumaclust Binary: sumaclust Architecture: any Version: 1.0.36+ds-2 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille , Pierre Gruet Homepage: http://metabarcoding.org/sumaclust Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/sumaclust Vcs-Git: https://salsa.debian.org/med-team/sumaclust.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libsuma-dev Package-List: sumaclust deb science optional arch=any Checksums-Sha1: 73b85f10a7a36b7835df4aa5932d5b338e653d0e 109149 sumaclust_1.0.36+ds.orig.tar.gz 507d9504c32cee84118320011c1a2ae38ebbb335 12392 sumaclust_1.0.36+ds-2.debian.tar.xz Checksums-Sha256: c4a8df2f35bb3aee60956de5f42b8ddc0ecd9cc6d0fc7aed9834d9ba48831706 109149 sumaclust_1.0.36+ds.orig.tar.gz 65852219971f49e1cac2871785c272c09363562cb7318b58388737db7f0653d4 12392 sumaclust_1.0.36+ds-2.debian.tar.xz Files: cdb3c377e8e18981b1ec9cc25810db2f 109149 sumaclust_1.0.36+ds.orig.tar.gz 26b8bafcf8f764aa3c1d3762186e54df 12392 sumaclust_1.0.36+ds-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmLN7DIACgkQYAMWptwn dHa8bw/+L0jxmB0Mv3cs8JJJWqIklJDe59+qABhg2h+QumxdNIsGRKFnLQqgmeIJ 4ZIkMMTjmEPNUG6XnFrSflMIgXnw8RovUt2F8d87/cxvQKNlTDC7IUypURh+FIJz /gicq0QZ2lzc6vGHHrosPZQ53bQ98wnbHpyBej+NUzjbY8b1XO5hvxqAiMNeiF5p XOdlRXeSNOoqNnypSSUsUdIo3A5osj70avlx7iM57wDEJPvr1xM5ia3f1A2GWgg/ 3BhdNSvBQCwh4t9j5Ub1q83qIlK4MkYlPhCrR6jN+W6mFfXD75CjEZzPu2SysWy8 wYY3eY/yOXh5gLp/IZ+zaffOFu5l6/oZdCGSf4WtDR+8hiZ08VWSj6tMowGuTsTf A7dxWKcbiR8G0/c0yRneVdQMlaDaGPXP9tIaKchHNx+sORD9l7JWQi70iNBTiw1C I1JS02QJa5v2hl6/n31PYF1YkRabeEi5z/uF5il6HRBgsToHdYCdsKjoBDPGLy+U 4zR0pcV3/WbMgl9oGLOkl2jVzJJRdjW823RblTRbCYjFoDMNxetrrshm5TS296Dg JOT/zuxZmzE2khSy4OVuohp7bP0JLZ/81g56KmYumTgL9cGI5ezWWN/QvGnSNcne aFARzBn6y9Uo6xLgiAlTeL8kVj+QVuJ7wxPLi+XE6Gaoeb87mRE= =5cOD -----END PGP SIGNATURE----- Sun Nov 24 15:38:12 UTC 2024 I: Checking whether the package is not for us Sun Nov 24 15:38:12 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sun Nov 24 15:38:12 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sun Nov 24 15:38:12 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sun Nov 24 15:38:12 UTC 2024 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-9GwXbS' ==================================================================================== Sun Nov 24 15:38:13 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 sumaclust unstable /srv/reproducible-results/rbuild-debian/r-b-build.GI0XYwvi 1.0.36+ds-2" as arguments. Sun Nov 24 15:38:13 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-PMDFFfMU" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sun Nov 24 15:38:13 UTC 2024 I: Downloading source for unstable/sumaclust=1.0.36+ds-2 Reading package lists... NOTICE: 'sumaclust' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/sumaclust.git Please use: git clone https://salsa.debian.org/med-team/sumaclust.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 124 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main sumaclust 1.0.36+ds-2 (dsc) [2050 B] Get:2 http://deb.debian.org/debian unstable/main sumaclust 1.0.36+ds-2 (tar) [109 kB] Get:3 http://deb.debian.org/debian unstable/main sumaclust 1.0.36+ds-2 (diff) [12.4 kB] Fetched 124 kB in 0s (5503 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'sumaclust' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/sumaclust.git Please use: git clone https://salsa.debian.org/med-team/sumaclust.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 124 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main sumaclust 1.0.36+ds-2 (dsc) [2050 B] Get:2 http://deb.debian.org/debian unstable/main sumaclust 1.0.36+ds-2 (tar) [109 kB] Get:3 http://deb.debian.org/debian unstable/main sumaclust 1.0.36+ds-2 (diff) [12.4 kB] Fetched 124 kB in 0s (5503 kB/s) Download complete and in download only mode ============================================================================= Building sumaclust in unstable on arm64 on codethink04-arm64 now. Date: Sun Nov 24 15:38:14 GMT 2024 Date UTC: Sun Nov 24 15:38:14 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 24 03:38:14 -12 2024 I: pbuilder-time-stamp: 1732462694 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [sumaclust_1.0.36+ds-2.dsc] I: copying [./sumaclust_1.0.36+ds.orig.tar.gz] I: copying [./sumaclust_1.0.36+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jul 12 21:48:34 2022 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sumaclust_1.0.36+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting sumaclust in sumaclust-1.0.36+ds dpkg-source: info: unpacking sumaclust_1.0.36+ds.orig.tar.gz dpkg-source: info: unpacking sumaclust_1.0.36+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_build.patch dpkg-source: info: applying use_debian_packaged_sumalibs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3062544/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='e0a01609407b40ea89e4bb34268e2155' 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='3062544' 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.GI0XYwvi/pbuilderrc_zgZf --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GI0XYwvi/b1 --logfile b1/build.log sumaclust_1.0.36+ds-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3062544/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libsuma-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 ... 20084 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 libsuma-dev; however: Package libsuma-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} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsuma-dev{a} libsuma1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 19.5 MB of archives. After unpacking 78.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libsuma1 arm64 1.0.36-3+b1 [28.9 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libsuma-dev arm64 1.0.36-3+b1 [39.6 kB] Fetched 19.5 MB in 0s (91.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../23-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libsuma1. Preparing to unpack .../29-libsuma1_1.0.36-3+b1_arm64.deb ... Unpacking libsuma1 (1.0.36-3+b1) ... Selecting previously unselected package libsuma-dev. Preparing to unpack .../30-libsuma-dev_1.0.36-3+b1_arm64.deb ... Unpacking libsuma-dev (1.0.36-3+b1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libsuma1 (1.0.36-3+b1) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libsuma-dev (1.0.36-3+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-4) ... 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/sumaclust-1.0.36+ds/ && 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 > ../sumaclust_1.0.36+ds-2_source.changes dpkg-buildpackage: info: source package sumaclust dpkg-buildpackage: info: source version 1.0.36+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/sumaclust-1.0.36+ds' rm -f sumaclust.o mtcompare_sumaclust.o rm -f sumaclust make[1]: Leaving directory '/build/reproducible-path/sumaclust-1.0.36+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/sumaclust-1.0.36+ds' gcc -I/usr/include -g -O3 -s -DOMP_SUPPORT -fopenmp -w -I/build/reproducible-path/sumaclust-1.0.36+ds/sumalibs -c -o sumaclust.o sumaclust.c -lsuma -lm gcc -I/usr/include -g -O3 -s -DOMP_SUPPORT -fopenmp -w -I/build/reproducible-path/sumaclust-1.0.36+ds/sumalibs -c -o mtcompare_sumaclust.o mtcompare_sumaclust.c -lsuma -lm sumaclust.c: In function 'printInBIOMformat': sumaclust.c:294:27: error: assignment to 'struct **' from incompatible pointer type 'struct fastaSeqPtr *' [-Wincompatible-pointer-types] 294 | c = (*seq)->center; | ^ sumaclust.c: In function 'printInOTUtableFormat': sumaclust.c:461:27: error: assignment to 'struct **' from incompatible pointer type 'struct fastaSeqPtr *' [-Wincompatible-pointer-types] 461 | c = (*seq)->center; | ^ sumaclust.c: In function 'putSeqInCluster': sumaclust.c:583:24: error: assignment to 'struct fastaSeqPtr *' from incompatible pointer type 'struct **' [-Wincompatible-pointer-types] 583 | (*seq)->center = center; | ^ mtcompare_sumaclust.c: In function 'putSeqInClusterMT': mtcompare_sumaclust.c:68:26: error: assignment to 'struct fastaSeqPtr *' from incompatible pointer type 'struct **' [-Wincompatible-pointer-types] 68 | pseq->center = db+center_idx; | ^ mtcompare_sumaclust.c: In function 'initializeCentersAndScores': sumaclust.c: In function 'computeClusterWeights': sumaclust.c:750:24: error: assignment to 'struct **' from incompatible pointer type 'struct fastaSeqPtr *' [-Wincompatible-pointer-types] 750 | center = (*seq)->center; | ^ sumaclust.c:763:24: error: assignment to 'struct **' from incompatible pointer type 'struct fastaSeqPtr *' [-Wincompatible-pointer-types] 763 | center = (*seq)->center; | ^ sumaclust.c: In function 'main': mtcompare_sumaclust.c:230:41: error: assignment to 'struct fastaSeqPtr *' from incompatible pointer type 'struct **' [-Wincompatible-pointer-types] 230 | (*db_i)->center = (control->db)+i; | ^ sumaclust.c:1001:42: error: assignment to 'struct fastaSeqPtr *' from incompatible pointer type 'fastaSeqPtr' {aka 'struct *'} [-Wincompatible-pointer-types] 1001 | ((db.fastaSeqs)+i)->next = (db.fastaSeqs)+i-1; | ^ sumaclust.c:1009:73: error: passing argument 4 of 'qsort' from incompatible pointer type [-Wincompatible-pointer-types] 1009 | qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), sortSeqsWithCounts); | ^~~~~~~~~~~~~~~~~~ | | | int (*)(const void **, const void **) In file included from sumaclust.c:9: /usr/include/stdlib.h:971:34: note: expected '__compar_fn_t' {aka 'int (*)(const void *, const void *)'} but argument is of type 'int (*)(const void **, const void **)' 971 | __compar_fn_t __compar) __nonnull ((1, 4)); | ~~~~~~~~~~~~~~^~~~~~~~ sumaclust.c:1011:73: error: passing argument 4 of 'qsort' from incompatible pointer type [-Wincompatible-pointer-types] 1011 | qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), reverseSortSeqsWithCounts); | ^~~~~~~~~~~~~~~~~~~~~~~~~ | | | int (*)(const void **, const void **) /usr/include/stdlib.h:971:34: note: expected '__compar_fn_t' {aka 'int (*)(const void *, const void *)'} but argument is of type 'int (*)(const void **, const void **)' 971 | __compar_fn_t __compar) __nonnull ((1, 4)); | ~~~~~~~~~~~~~~^~~~~~~~ sumaclust.c:1017:73: error: passing argument 4 of 'qsort' from incompatible pointer type [-Wincompatible-pointer-types] 1017 | qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), sortSeqsP); | ^~~~~~~~~ | | | int (*)(const void **, const void **) /usr/include/stdlib.h:971:34: note: expected '__compar_fn_t' {aka 'int (*)(const void *, const void *)'} but argument is of type 'int (*)(const void **, const void **)' 971 | __compar_fn_t __compar) __nonnull ((1, 4)); | ~~~~~~~~~~~~~~^~~~~~~~ sumaclust.c:1019:73: error: passing argument 4 of 'qsort' from incompatible pointer type [-Wincompatible-pointer-types] 1019 | qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), reverseSortSeqsP); | ^~~~~~~~~~~~~~~~ | | | int (*)(const void **, const void **) /usr/include/stdlib.h:971:34: note: expected '__compar_fn_t' {aka 'int (*)(const void *, const void *)'} but argument is of type 'int (*)(const void **, const void **)' 971 | __compar_fn_t __compar) __nonnull ((1, 4)); | ~~~~~~~~~~~~~~^~~~~~~~ sumaclust.c:1049:61: error: passing argument 2 of 'printSeq' from incompatible pointer type [-Wincompatible-pointer-types] 1049 | printSeq(uniqSeqs+i, (*(uniqSeqs+i))->center, (*(uniqSeqs+i))->score, FASTA_output); | ~~~~~~~~~~~~~~~^~~~~~~~ | | | struct fastaSeqPtr * sumaclust.c:512:46: note: expected 'struct **' but argument is of type 'struct fastaSeqPtr *' 512 | void printSeq(fastaSeqPtr* seq, fastaSeqPtr* center, double score, FILE* output) | ~~~~~~~~~~~~~^~~~~~ make[1]: *** [global.mk:20: mtcompare_sumaclust.o] Error 1 make[1]: *** Waiting for unfinished jobs.... make[1]: *** [global.mk:20: sumaclust.o] Error 1 make[1]: Leaving directory '/build/reproducible-path/sumaclust-1.0.36+ds' dh_auto_build: error: make -j12 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:10: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/3062544 and its subdirectories Starting cleanup. All cleanup done. Sun Nov 24 15:38:49 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-PMDFFfMU, removing. /srv/reproducible-results/rbuild-debian/r-b-build.GI0XYwvi: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 24 15:38 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 24 15:38 b2 -rw------- 1 jenkins jenkins 3196 Nov 24 15:38 rbuildlog.wpsqs3I -rw-r--r-- 1 jenkins jenkins 2050 Jul 12 2022 sumaclust_1.0.36+ds-2.dsc /srv/reproducible-results/rbuild-debian/r-b-build.GI0XYwvi/b1: total 28 -rw-r--r-- 1 jenkins jenkins 24735 Nov 24 15:38 build.log /srv/reproducible-results/rbuild-debian/r-b-build.GI0XYwvi/b2: total 0 Sun Nov 24 15:38:50 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 24 03:38:14 -12 2024 I: pbuilder-time-stamp: 1732462694 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [sumaclust_1.0.36+ds-2.dsc] I: copying [./sumaclust_1.0.36+ds.orig.tar.gz] I: copying [./sumaclust_1.0.36+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jul 12 21:48:34 2022 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sumaclust_1.0.36+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting sumaclust in sumaclust-1.0.36+ds dpkg-source: info: unpacking sumaclust_1.0.36+ds.orig.tar.gz dpkg-source: info: unpacking sumaclust_1.0.36+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying fix_build.patch dpkg-source: info: applying use_debian_packaged_sumalibs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3062544/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='e0a01609407b40ea89e4bb34268e2155' 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='3062544' 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.GI0XYwvi/pbuilderrc_zgZf --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GI0XYwvi/b1 --logfile b1/build.log sumaclust_1.0.36+ds-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3062544/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libsuma-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 ... 20084 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 libsuma-dev; however: Package libsuma-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} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsuma-dev{a} libsuma1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 19.5 MB of archives. After unpacking 78.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libsuma1 arm64 1.0.36-3+b1 [28.9 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libsuma-dev arm64 1.0.36-3+b1 [39.6 kB] Fetched 19.5 MB in 0s (91.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20084 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. 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Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-4) ... 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/sumaclust-1.0.36+ds/ && 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 > ../sumaclust_1.0.36+ds-2_source.changes dpkg-buildpackage: info: source package sumaclust dpkg-buildpackage: info: source version 1.0.36+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/sumaclust-1.0.36+ds' rm -f sumaclust.o mtcompare_sumaclust.o rm -f sumaclust make[1]: Leaving directory '/build/reproducible-path/sumaclust-1.0.36+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/sumaclust-1.0.36+ds' gcc -I/usr/include -g -O3 -s -DOMP_SUPPORT -fopenmp -w -I/build/reproducible-path/sumaclust-1.0.36+ds/sumalibs -c -o sumaclust.o sumaclust.c -lsuma -lm gcc -I/usr/include -g -O3 -s -DOMP_SUPPORT -fopenmp -w -I/build/reproducible-path/sumaclust-1.0.36+ds/sumalibs -c -o mtcompare_sumaclust.o mtcompare_sumaclust.c -lsuma -lm sumaclust.c: In function 'printInBIOMformat': sumaclust.c:294:27: error: assignment to 'struct **' from incompatible pointer type 'struct fastaSeqPtr *' [-Wincompatible-pointer-types] 294 | c = (*seq)->center; | ^ sumaclust.c: In function 'printInOTUtableFormat': sumaclust.c:461:27: error: assignment to 'struct **' from incompatible pointer type 'struct fastaSeqPtr *' [-Wincompatible-pointer-types] 461 | c = (*seq)->center; | ^ sumaclust.c: In function 'putSeqInCluster': sumaclust.c:583:24: error: assignment to 'struct fastaSeqPtr *' from incompatible pointer type 'struct **' [-Wincompatible-pointer-types] 583 | (*seq)->center = center; | ^ mtcompare_sumaclust.c: In function 'putSeqInClusterMT': mtcompare_sumaclust.c:68:26: error: assignment to 'struct fastaSeqPtr *' from incompatible pointer type 'struct **' [-Wincompatible-pointer-types] 68 | pseq->center = db+center_idx; | ^ mtcompare_sumaclust.c: In function 'initializeCentersAndScores': sumaclust.c: In function 'computeClusterWeights': sumaclust.c:750:24: error: assignment to 'struct **' from incompatible pointer type 'struct fastaSeqPtr *' [-Wincompatible-pointer-types] 750 | center = (*seq)->center; | ^ sumaclust.c:763:24: error: assignment to 'struct **' from incompatible pointer type 'struct fastaSeqPtr *' [-Wincompatible-pointer-types] 763 | center = (*seq)->center; | ^ sumaclust.c: In function 'main': mtcompare_sumaclust.c:230:41: error: assignment to 'struct fastaSeqPtr *' from incompatible pointer type 'struct **' [-Wincompatible-pointer-types] 230 | (*db_i)->center = (control->db)+i; | ^ sumaclust.c:1001:42: error: assignment to 'struct fastaSeqPtr *' from incompatible pointer type 'fastaSeqPtr' {aka 'struct *'} [-Wincompatible-pointer-types] 1001 | ((db.fastaSeqs)+i)->next = (db.fastaSeqs)+i-1; | ^ sumaclust.c:1009:73: error: passing argument 4 of 'qsort' from incompatible pointer type [-Wincompatible-pointer-types] 1009 | qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), sortSeqsWithCounts); | ^~~~~~~~~~~~~~~~~~ | | | int (*)(const void **, const void **) In file included from sumaclust.c:9: /usr/include/stdlib.h:971:34: note: expected '__compar_fn_t' {aka 'int (*)(const void *, const void *)'} but argument is of type 'int (*)(const void **, const void **)' 971 | __compar_fn_t __compar) __nonnull ((1, 4)); | ~~~~~~~~~~~~~~^~~~~~~~ sumaclust.c:1011:73: error: passing argument 4 of 'qsort' from incompatible pointer type [-Wincompatible-pointer-types] 1011 | qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), reverseSortSeqsWithCounts); | ^~~~~~~~~~~~~~~~~~~~~~~~~ | | | int (*)(const void **, const void **) /usr/include/stdlib.h:971:34: note: expected '__compar_fn_t' {aka 'int (*)(const void *, const void *)'} but argument is of type 'int (*)(const void **, const void **)' 971 | __compar_fn_t __compar) __nonnull ((1, 4)); | ~~~~~~~~~~~~~~^~~~~~~~ sumaclust.c:1017:73: error: passing argument 4 of 'qsort' from incompatible pointer type [-Wincompatible-pointer-types] 1017 | qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), sortSeqsP); | ^~~~~~~~~ | | | int (*)(const void **, const void **) /usr/include/stdlib.h:971:34: note: expected '__compar_fn_t' {aka 'int (*)(const void *, const void *)'} but argument is of type 'int (*)(const void **, const void **)' 971 | __compar_fn_t __compar) __nonnull ((1, 4)); | ~~~~~~~~~~~~~~^~~~~~~~ sumaclust.c:1019:73: error: passing argument 4 of 'qsort' from incompatible pointer type [-Wincompatible-pointer-types] 1019 | qsort((void*) uniqSeqs, n, sizeof(fastaSeqPtr), reverseSortSeqsP); | ^~~~~~~~~~~~~~~~ | | | int (*)(const void **, const void **) /usr/include/stdlib.h:971:34: note: expected '__compar_fn_t' {aka 'int (*)(const void *, const void *)'} but argument is of type 'int (*)(const void **, const void **)' 971 | __compar_fn_t __compar) __nonnull ((1, 4)); | ~~~~~~~~~~~~~~^~~~~~~~ sumaclust.c:1049:61: error: passing argument 2 of 'printSeq' from incompatible pointer type [-Wincompatible-pointer-types] 1049 | printSeq(uniqSeqs+i, (*(uniqSeqs+i))->center, (*(uniqSeqs+i))->score, FASTA_output); | ~~~~~~~~~~~~~~~^~~~~~~~ | | | struct fastaSeqPtr * sumaclust.c:512:46: note: expected 'struct **' but argument is of type 'struct fastaSeqPtr *' 512 | void printSeq(fastaSeqPtr* seq, fastaSeqPtr* center, double score, FILE* output) | ~~~~~~~~~~~~~^~~~~~ make[1]: *** [global.mk:20: mtcompare_sumaclust.o] Error 1 make[1]: *** Waiting for unfinished jobs.... make[1]: *** [global.mk:20: sumaclust.o] Error 1 make[1]: Leaving directory '/build/reproducible-path/sumaclust-1.0.36+ds' dh_auto_build: error: make -j12 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:10: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/3062544 and its subdirectories sumaclust failed to build from source. removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/sumaclust_1.0.36+ds-2.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/sumaclust_1.0.36+ds-2.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/sumaclust_1.0.36+ds-2.build1.log.gz' Sun Nov 24 15:38:51 UTC 2024 W: No second build log, what happened? Compressing the 1st log... b1/build.log: 77.8% -- replaced with stdout INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-24 15:38:52] INFO: Starting at 2024-11-24 15:38:52.701012 [2024-11-24 15:38:52] INFO: Generating the pages of 1 package(s) [2024-11-24 15:38:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/sumaclust_1.0.36+ds-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/sumaclust_1.0.36+ds-2.diff.gz is missing [2024-11-24 15:38:53] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/sumaclust didn't produce a buildlog, even though it has been built. [2024-11-24 15:38:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/sumaclust_1.0.36+ds-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/sumaclust_1.0.36+ds-2.diff.gz is missing [2024-11-24 15:38:53] INFO: Finished at 2024-11-24 15:38:53.211431, took: 0:00:00.510429 Sun Nov 24 15:38:53 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/sumaclust.html Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/sumaclust_1.0.36+ds-2.rbuild.log: 74.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/sumaclust_1.0.36+ds-2.rbuild.log.gz [2024-11-24 15:38:53] INFO: Starting at 2024-11-24 15:38:53.611400 [2024-11-24 15:38:53] INFO: Generating the pages of 1 package(s) [2024-11-24 15:38:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/sumaclust_1.0.36+ds-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/sumaclust_1.0.36+ds-2.diff.gz is missing [2024-11-24 15:38:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/sumaclust_1.0.36+ds-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/sumaclust_1.0.36+ds-2.diff.gz is missing [2024-11-24 15:38:53] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/i386/sumaclust_1.0.36+ds-2.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/i386/sumaclust_1.0.36+ds-2.diff.gz is missing [2024-11-24 15:38:54] INFO: Finished at 2024-11-24 15:38:54.000727, took: 0:00:00.389332 All cleanup done. Sun Nov 24 15:38:54 UTC 2024 - total duration: 0h 0m 58s. Sun Nov 24 15:38:54 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-Qm5vKXRX, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1min 35ms CPU time consumed: 5.083s