Tue Apr 18 02:44:49 UTC 2023 I: starting to build kma/bookworm/arm64 on jenkins on '2023-04-18 02:43' Tue Apr 18 02:44:49 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_12/6497/console.log Tue Apr 18 02:44:49 UTC 2023 I: Downloading source for bookworm/kma=1.4.11-1 --2023-04-18 02:44:49-- http://cdn-fastly.deb.debian.org/debian/pool/main/k/kma/kma_1.4.11-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1440 (1.4K) [text/prs.lines.tag] Saving to: ‘kma_1.4.11-1.dsc’ 0K . 100% 49.1M=0s 2023-04-18 02:44:49 (49.1 MB/s) - ‘kma_1.4.11-1.dsc’ saved [1440/1440] Tue Apr 18 02:44:49 UTC 2023 I: kma_1.4.11-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: kma Binary: kma Architecture: any-amd64 arm64 mips64el ppc64el s390x alpha ia64 ppc64 riscv64 sparc64 Version: 1.4.11-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://bitbucket.org/genomicepidemiology/kma Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/kma Vcs-Git: https://salsa.debian.org/med-team/kma.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev Package-List: kma deb science optional arch=any-amd64,arm64,mips64el,ppc64el,s390x,alpha,ia64,ppc64,riscv64,sparc64 Checksums-Sha1: 1c4f2ea14ec15d83d0b418bca2e37970ff9f0833 622768 kma_1.4.11.orig.tar.xz e1968901cdf051980f21618453a3d6671b086b69 6572 kma_1.4.11-1.debian.tar.xz Checksums-Sha256: 2a6e2f28d9a7d1ec2877294103885fc272dee173e2e5790321097a43ba6cef36 622768 kma_1.4.11.orig.tar.xz e579d68e3c8dd383906752e194bc26dfc4988ba045630b344141ea2358e4cc4b 6572 kma_1.4.11-1.debian.tar.xz Files: 24a8c1a25b61bf5d9dec8f1f576d4fb2 622768 kma_1.4.11.orig.tar.xz afdf3b2dd1acaa22fa49bdf4ee7e269c 6572 kma_1.4.11-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iHUEARYIAB0WIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCY9Y+oAAKCRAqJ5BL1yQ+ 2p4mAP9DPbBarV48/okY7wrEXiXrMxMxHgm3XJUfML8MtubqrgEAxgNEZb1ZJluH jXRO6VkcEldwvf58yPe+NgqJPnVheQ8= =bnrv -----END PGP SIGNATURE----- Tue Apr 18 02:44:49 UTC 2023 I: Checking whether the package is not for us Tue Apr 18 02:44:49 UTC 2023 I: Starting 1st build on remote node codethink11-arm64.debian.net. Tue Apr 18 02:44:49 UTC 2023 I: Preparing to do remote build '1' on codethink11-arm64.debian.net. Tue Apr 18 02:47:26 UTC 2023 I: Deleting $TMPDIR on codethink11-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 19 21:08:41 -12 2024 I: pbuilder-time-stamp: 1716196121 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [kma_1.4.11-1.dsc] I: copying [./kma_1.4.11.orig.tar.xz] I: copying [./kma_1.4.11-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Jan 28 21:38:40 2023 -12 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./kma_1.4.11-1.dsc: no acceptable signature found dpkg-source: info: extracting kma in kma-1.4.11 dpkg-source: info: unpacking kma_1.4.11.orig.tar.xz dpkg-source: info: unpacking kma_1.4.11-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying blhc.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/428/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' 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=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='428' 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.EKvHOog6/pbuilderrc_d8TU --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.EKvHOog6/b1 --logfile b1/build.log kma_1.4.11-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink11-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 18 04:48 /bin -> usr/bin I: user script /srv/workspace/pbuilder/428/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 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. 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} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{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 19.3 MB of archives. After unpacking 75.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Fetched 19.3 MB in 0s (47.2 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 ... 19616 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../22-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.1+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-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 .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../30-zlib1g-dev_1%3a1.2.13.dfsg-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-8) ... 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/kma-1.4.11/ && 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 > ../kma_1.4.11-1_source.changes dpkg-buildpackage: info: source package kma dpkg-buildpackage: info: source version 1.4.11-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j8 clean make[1]: Entering directory '/build/kma-1.4.11' rm -f align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o conclave.o db.o decon.o dist.o ef.o filebuff.o frags.o hashmap.o hashmapcci.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmers.o kmmap.o loadupdate.o makeindex.o matrix.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o trim.o tmp.o tsv.o update.o updateindex.o updatescores.o valueshash.o vcf.o xml.o kma kma_index kma_shm kma_update libkma.a make[1]: Leaving directory '/build/kma-1.4.11' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/kma-1.4.11' cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o align.o align.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o alnfrags.o alnfrags.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ankers.o ankers.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o assembly.o assembly.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o chain.o chain.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compdna.o compdna.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compkmers.o compkmers.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o compress.o compress.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o conclave.o conclave.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o db.o db.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o decon.o decon.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dist.o dist.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ef.o ef.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filebuff.o filebuff.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o frags.o frags.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmap.o hashmap.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapcci.o hashmapcci.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapkma.o hashmapkma.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashmapkmers.o hashmapkmers.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o index.o index.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kma.o kma.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmapipe.o kmapipe.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmeranker.o kmeranker.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmers.o kmers.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kmmap.o kmmap.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o loadupdate.o loadupdate.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o makeindex.o makeindex.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o matrix.o matrix.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mt1.o mt1.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o nw.o nw.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o pherror.o pherror.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o printconsensus.o printconsensus.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qseqs.o qseqs.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o qualcheck.o qualcheck.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o runinput.o runinput.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o runkma.o runkma.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o savekmers.o savekmers.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seq2fasta.o seq2fasta.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqmenttree.o seqmenttree.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seqparse.o seqparse.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o shm.o shm.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sparse.o sparse.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o spltdb.o spltdb.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stdnuc.o stdnuc.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stdstat.o stdstat.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o trim.o trim.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp.o tmp.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tsv.o tsv.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o update.o update.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o updateindex.o updateindex.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o updatescores.o updatescores.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o valueshash.o valueshash.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o vcf.o vcf.c cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o xml.o xml.c ar -csr libkma.a align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o conclave.o db.o decon.o dist.o ef.o filebuff.o frags.o hashmap.o hashmapcci.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmers.o kmmap.o loadupdate.o makeindex.o matrix.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o trim.o tmp.o tsv.o update.o updateindex.o updatescores.o valueshash.o vcf.o xml.o cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -o kma main.c libkma.a -lm -lpthread -lz -Wl,-z,relro -Wl,-z,now cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -o kma_index kma_index.c libkma.a -lm -lz -Wl,-z,relro -Wl,-z,now cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -o kma_shm kma_shm.c libkma.a -Wl,-z,relro -Wl,-z,now cc -g -O2 -ffile-prefix-map=/build/kma-1.4.11=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -Wdate-time -D_FORTIFY_SOURCE=2 -o kma_update kma_update.c libkma.a -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/kma-1.4.11' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/kma/ dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/kma/usr/bin/kma: DWARF compression not beneficial - old size 458486 new size 461215 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'kma' in '../kma_1.4.11-1_arm64.deb'. dpkg-deb: building package 'kma-dbgsym' in '../kma-dbgsym_1.4.11-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../kma_1.4.11-1_arm64.buildinfo dpkg-genchanges --build=binary -O../kma_1.4.11-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full 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/428 and its subdirectories I: Current time: Sun May 19 21:09:59 -12 2024 I: pbuilder-time-stamp: 1716196199 Tue Apr 18 02:47:52 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink16-arm64.debian.net. Tue Apr 18 02:47:52 UTC 2023 I: Preparing to do remote build '2' on codethink16-arm64.debian.net. Tue Apr 18 02:50:32 UTC 2023 I: Deleting $TMPDIR on codethink16-arm64.debian.net. Tue Apr 18 02:50:58 UTC 2023 I: kma_1.4.11-1_arm64.changes: Format: 1.8 Date: Sun, 29 Jan 2023 15:05:28 +0530 Source: kma Binary: kma kma-dbgsym Architecture: arm64 Version: 1.4.11-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: kma - mapping genomic sequences to raw reads directly against redundant Changes: kma (1.4.11-1) unstable; urgency=medium . * Team Upload. * New upstream version 1.4.11 Checksums-Sha1: 177ca10ff786de51407ac7d04c5629c462fbf620 678048 kma-dbgsym_1.4.11-1_arm64.deb 4f93b1b5872176f1017d280ac53d74a4d175ffed 5122 kma_1.4.11-1_arm64.buildinfo 4c66dce44a1e67fcd7a611f4c4d93e2a5e56c928 200800 kma_1.4.11-1_arm64.deb Checksums-Sha256: f7a02d823db06d67d3f7c4109970317d78da43c30ac5766d8d44ba506107eb7a 678048 kma-dbgsym_1.4.11-1_arm64.deb 8e1d4e17e0b182277860a23869d1739bf7b6aa3eb3736bf4c7542cb990a9b790 5122 kma_1.4.11-1_arm64.buildinfo f717abf676dee422940e4fbbac6d8121cca761a61376a881bb88dea026a04746 200800 kma_1.4.11-1_arm64.deb Files: 0fe7b2c7c61f8dd57f4d865793d3881f 678048 debug optional kma-dbgsym_1.4.11-1_arm64.deb cfb5f89b48950c36714a86cf77f35887 5122 science optional kma_1.4.11-1_arm64.buildinfo 99353da7ffb68be8cd6ee830b3791a5b 200800 science optional kma_1.4.11-1_arm64.deb Tue Apr 18 02:50:59 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.EKvHOog6/kma_1.4.11-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.EKvHOog6/kma_1.4.11-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.EKvHOog6/kma_1.4.11-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.EKvHOog6/b1/kma_1.4.11-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.EKvHOog6/b2/kma_1.4.11-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.408s) 0.408s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.027s) 0.026s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Tue Apr 18 02:51:00 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 18 02:51:00 UTC 2023 I: kma from bookworm built successfully and reproducibly on arm64. Tue Apr 18 02:51:01 UTC 2023 I: Submitting .buildinfo files to external archives: Tue Apr 18 02:51:01 UTC 2023 I: Submitting 8.0K b1/kma_1.4.11-1_arm64.buildinfo.asc Tue Apr 18 02:51:03 UTC 2023 I: Submitting 8.0K b2/kma_1.4.11-1_arm64.buildinfo.asc Tue Apr 18 02:51:04 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 18 02:51:04 UTC 2023 I: Done submitting .buildinfo files. Tue Apr 18 02:51:04 UTC 2023 I: Removing signed kma_1.4.11-1_arm64.buildinfo.asc files: removed './b1/kma_1.4.11-1_arm64.buildinfo.asc' removed './b2/kma_1.4.11-1_arm64.buildinfo.asc'