Sat May 11 12:34:06 UTC 2024 I: starting to build nxtrim/unstable/arm64 on jenkins on '2024-05-11 12:33' Sat May 11 12:34:06 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_22/10183/console.log Sat May 11 12:34:06 UTC 2024 I: Downloading source for unstable/nxtrim=0.4.3+dfsg-3 --2024-05-11 12:34:06-- http://deb.debian.org/debian/pool/main/n/nxtrim/nxtrim_0.4.3%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1983 (1.9K) [text/prs.lines.tag] Saving to: ‘nxtrim_0.4.3+dfsg-3.dsc’ 0K . 100% 201M=0s 2024-05-11 12:34:06 (201 MB/s) - ‘nxtrim_0.4.3+dfsg-3.dsc’ saved [1983/1983] Sat May 11 12:34:06 UTC 2024 I: nxtrim_0.4.3+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: nxtrim Binary: nxtrim Architecture: any Version: 0.4.3+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Nilesh Patra Homepage: https://github.com/sequencing/NxTrim Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/nxtrim Vcs-Git: https://salsa.debian.org/med-team/nxtrim.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev Package-List: nxtrim deb science optional arch=any Checksums-Sha1: 9a4f27ce5abe719114f9a9309e5e15118ed63c16 65903 nxtrim_0.4.3+dfsg.orig.tar.gz f6fd1e0f3906a1d41550703a2007dcd91eb4e15a 4956 nxtrim_0.4.3+dfsg-3.debian.tar.xz Checksums-Sha256: 3b1fdfc3a7296d0a54a622ecc0be4e9e25b513b762727fb066ad78795d171c04 65903 nxtrim_0.4.3+dfsg.orig.tar.gz 22931ef2727e020675e318316925c55482eaf981c2f3cbd6fb21c5a05b50575e 4956 nxtrim_0.4.3+dfsg-3.debian.tar.xz Files: be88d0019dd82dc1696dfd2d6c185c47 65903 nxtrim_0.4.3+dfsg.orig.tar.gz 13d59407de82767a54cb05f9422d201d 4956 nxtrim_0.4.3+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmOgg1URHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFttg//Zb1qzrAj6GL61xAcEgO6tvP5mqgyIh62 F2H1w8Zjmkx5l5p5/fH/MOiURdJekPG/tS1pfoLwznxCxbqsb4XMhD3/f+/Xztsz i2GHKDkgqqI688PJb3lv42IabdyI8Et4kQF10McYU//XHtftPwvK8UBwTl9Aztbh 8Zbee4mbU8en624D4ylUsY46JT84nav3bk9K3hX8s1HW6LicL0NBxqjR7hJZqFiJ /vIARj/8vlJO2YRwTY9gSJG6ytpKz7sIiGnMWaRaxnggmDbWVO0xRHL7BWLPlUfo 6escvle98KIdLfjQZDI+fsp2uQ6b6WJ8NA957SByCc2G9a7WP0ln24kL6U+/IVbR XgrZjP6In7fVjQXLl4A3CkaUpDeme1+d1OtG0qMcPUXzltco3JPrS+/613k+uune 8r2q42PRMOqzHUdRn63E1u0jmAyLkDD+Zl09id2Z/fkLrIrvBfTeVV2B/Ie2vVtf 9/eA4quCDwGMPRzcikd2Pk05YbAK96zt0mzOPZuf4rVmP/Jp47gVkAVrWpxtG0Gu 55Gsqd9BcNo6NA2X1Q17bCxWHIpXuZXmF4Gq56Y0t0RqGsgNINUOeLApVi9qzx3a VhhNlbutpyBbj31WD0lAL2xGYrk5sW5qlrINvpPHxDDoevxAFsW6Ft9NcKjpeGjb 0nxQUV+Hg88= =J1t5 -----END PGP SIGNATURE----- Sat May 11 12:34:06 UTC 2024 I: Checking whether the package is not for us Sat May 11 12:34:06 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sat May 11 12:34:06 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sat May 11 12:34:37 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 11 00:34:09 -12 2024 I: pbuilder-time-stamp: 1715430849 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 [nxtrim_0.4.3+dfsg-3.dsc] I: copying [./nxtrim_0.4.3+dfsg.orig.tar.gz] I: copying [./nxtrim_0.4.3+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Dec 19 15:29:25 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./nxtrim_0.4.3+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting nxtrim in nxtrim-0.4.3+dfsg dpkg-source: info: unpacking nxtrim_0.4.3+dfsg.orig.tar.gz dpkg-source: info: unpacking nxtrim_0.4.3+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do-not-remove-non-existing.patch dpkg-source: info: applying make-script-executable.patch dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1769259/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='9c31441d254a465589851bc2033014bf' 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='1769259' 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.xKYhEMph/pbuilderrc_fHLa --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.xKYhEMph/b1 --logfile b1/build.log nxtrim_0.4.3+dfsg-3.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 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 11 07:44 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1769259/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 ... 19744 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. 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} 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 19.6 MB of archives. After unpacking 77.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 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 2.71-3 [332 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 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [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 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Fetched 19.6 MB in 0s (131 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 ... 19744 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... 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_2.71-3_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_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... 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 libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... 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_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../30-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-10) ... 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/nxtrim-0.4.3+dfsg/ && 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 > ../nxtrim_0.4.3+dfsg-3_source.changes dpkg-buildpackage: info: source package nxtrim dpkg-buildpackage: info: source version 0.4.3+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/nxtrim-0.4.3+dfsg' make[1]: git: No such file or directory rm -f matepair.o fastqlib.o utilityfunc.o nxtrim version.h rm -rf test/output_dir/ rm -f test/*bam test/*pe.fastq.gz test/*mp.fastq.gz test/*unknown.fastq.gz make[1]: Leaving directory '/build/reproducible-path/nxtrim-0.4.3+dfsg' 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/nxtrim-0.4.3+dfsg' make[1]: git: No such file or directory g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/nxtrim-0.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o matepair.o matepair.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/nxtrim-0.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o fastqlib.o fastqlib.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/nxtrim-0.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o utilityfunc.o utilityfunc.cpp echo '#define VERSION "v0.4.3"' > version.h g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/nxtrim-0.4.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard nxtrim.cpp matepair.o fastqlib.o utilityfunc.o -lz -o nxtrim -Wl,-z,relro -Wl,-z,now make[1]: Leaving directory '/build/reproducible-path/nxtrim-0.4.3+dfsg' dh_auto_test make -j12 test make[1]: Entering directory '/build/reproducible-path/nxtrim-0.4.3+dfsg' make[1]: git: No such file or directory bash -e example/run_test.sh Output: example/ENA.*.fastq.gz Trimming: R1: example/ENA_R1.fastq.gz R2: example/ENA_R2.fastq.gz Trimming summary: 1 / 1 ( 100.00% ) reads passed chastity/purity filters. 0 / 1 ( 0.00% ) reads had multiple copies of adapter (filtered). 0 / 1 ( 0.00% ) read pairs were ignored because template length appeared less than read length 1 remaining reads were trimmed 0 / 1 ( 0.00% ) read pairs had MP orientation 1 / 1 ( 100.00% ) read pairs had PE orientation 0 / 1 ( 0.00% ) read pairs had unknown orientation 0 / 1 ( 0.00% ) were single end reads 0 / 1 ( 0.00% ) extra single end reads were generated from overhangs Output: example/example11.*.fastq.gz Trimming: R1: example/example11_R1.fastq.gz R2: example/example11_R2.fastq.gz WARNING: reads with differing lengths. Has this data already been processed with nxtrim? Trimming summary: 1 / 1 ( 100.00% ) reads passed chastity/purity filters. 0 / 1 ( 0.00% ) reads had multiple copies of adapter (filtered). 0 / 1 ( 0.00% ) read pairs were ignored because template length appeared less than read length 1 remaining reads were trimmed 0 / 1 ( 0.00% ) read pairs had MP orientation 0 / 1 ( 0.00% ) read pairs had PE orientation 1 / 1 ( 100.00% ) read pairs had unknown orientation 0 / 1 ( 0.00% ) were single end reads 0 / 1 ( 0.00% ) extra single end reads were generated from overhangs Output: example/EXTERNAL.*.fastq.gz Trimming: R1: example/EXTERNAL_R1.fastq.gz R2: example/EXTERNAL_R2.fastq.gz Trimming summary: 1 / 1 ( 100.00% ) reads passed chastity/purity filters. 0 / 1 ( 0.00% ) reads had multiple copies of adapter (filtered). 0 / 1 ( 0.00% ) read pairs were ignored because template length appeared less than read length 1 remaining reads were trimmed 0 / 1 ( 0.00% ) read pairs had MP orientation 1 / 1 ( 100.00% ) read pairs had PE orientation 0 / 1 ( 0.00% ) read pairs had unknown orientation 0 / 1 ( 0.00% ) were single end reads 0 / 1 ( 0.00% ) extra single end reads were generated from overhangs Output: example/FailPF.*.fastq.gz Trimming: R1: example/FailPF_R1.fastq.gz R2: example/FailPF_R2.fastq.gz Trimming summary: 0 / 1 ( 0.00% ) reads passed chastity/purity filters. 0 / 0 ( nan% ) reads had multiple copies of adapter (filtered). 0 / 0 ( nan% ) read pairs were ignored because template length appeared less than read length 0 remaining reads were trimmed 0 / 0 ( nan% ) read pairs had MP orientation 0 / 0 ( nan% ) read pairs had PE orientation 0 / 0 ( nan% ) read pairs had unknown orientation 0 / 0 ( nan% ) were single end reads 0 / 0 ( nan% ) extra single end reads were generated from overhangs Output: example/MP.*.fastq.gz Trimming: R1: example/MP_R1.fastq.gz R2: example/MP_R2.fastq.gz Trimming summary: 54 / 54 ( 100.00% ) reads passed chastity/purity filters. 0 / 54 ( 0.00% ) reads had multiple copies of adapter (filtered). 0 / 54 ( 0.00% ) read pairs were ignored because template length appeared less than read length 54 remaining reads were trimmed 54 / 54 ( 100.00% ) read pairs had MP orientation 0 / 54 ( 0.00% ) read pairs had PE orientation 0 / 54 ( 0.00% ) read pairs had unknown orientation 0 / 54 ( 0.00% ) were single end reads 0 / 54 ( 0.00% ) extra single end reads were generated from overhangs Output: example/PE.*.fastq.gz Trimming: R1: example/PE_R1.fastq.gz R2: example/PE_R2.fastq.gz Trimming summary: 55 / 55 ( 100.00% ) reads passed chastity/purity filters. 0 / 55 ( 0.00% ) reads had multiple copies of adapter (filtered). 1 / 55 ( 1.82% ) read pairs were ignored because template length appeared less than read length 54 remaining reads were trimmed 0 / 54 ( 0.00% ) read pairs had MP orientation 54 / 54 ( 100.00% ) read pairs had PE orientation 0 / 54 ( 0.00% ) read pairs had unknown orientation 0 / 54 ( 0.00% ) were single end reads 0 / 54 ( 0.00% ) extra single end reads were generated from overhangs Output: example/sample.*.fastq.gz Trimming: R1: example/sample_R1.fastq.gz R2: example/sample_R2.fastq.gz Trimming summary: 163 / 163 ( 100.00% ) reads passed chastity/purity filters. 0 / 163 ( 0.00% ) reads had multiple copies of adapter (filtered). 1 / 163 ( 0.61% ) read pairs were ignored because template length appeared less than read length 162 remaining reads were trimmed 54 / 162 ( 33.33% ) read pairs had MP orientation 54 / 162 ( 33.33% ) read pairs had PE orientation 54 / 162 ( 33.33% ) read pairs had unknown orientation 0 / 162 ( 0.00% ) were single end reads 0 / 162 ( 0.00% ) extra single end reads were generated from overhangs Output: example/UNKNOWN.*.fastq.gz Trimming: R1: example/UNKNOWN_R1.fastq.gz R2: example/UNKNOWN_R2.fastq.gz Trimming summary: 54 / 54 ( 100.00% ) reads passed chastity/purity filters. 0 / 54 ( 0.00% ) reads had multiple copies of adapter (filtered). 0 / 54 ( 0.00% ) read pairs were ignored because template length appeared less than read length 54 remaining reads were trimmed 0 / 54 ( 0.00% ) read pairs had MP orientation 0 / 54 ( 0.00% ) read pairs had PE orientation 54 / 54 ( 100.00% ) read pairs had unknown orientation 0 / 54 ( 0.00% ) were single end reads 0 / 54 ( 0.00% ) extra single end reads were generated from overhangs make[1]: Leaving directory '/build/reproducible-path/nxtrim-0.4.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/nxtrim/ dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'nxtrim' in '../nxtrim_0.4.3+dfsg-3_arm64.deb'. dpkg-deb: building package 'nxtrim-dbgsym' in '../nxtrim-dbgsym_0.4.3+dfsg-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../nxtrim_0.4.3+dfsg-3_arm64.buildinfo dpkg-genchanges --build=binary -O../nxtrim_0.4.3+dfsg-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1769259 and its subdirectories I: Current time: Sat May 11 00:34:35 -12 2024 I: pbuilder-time-stamp: 1715430875 Sat May 11 12:34:37 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink02-arm64.debian.net. Sat May 11 12:34:37 UTC 2024 I: Preparing to do remote build '2' on codethink02-arm64.debian.net. Sat May 11 12:35:46 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. Sat May 11 12:35:47 UTC 2024 I: nxtrim_0.4.3+dfsg-3_arm64.changes: Format: 1.8 Date: Mon, 19 Dec 2022 16:27:49 +0100 Source: nxtrim Binary: nxtrim nxtrim-dbgsym Architecture: arm64 Version: 0.4.3+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: nxtrim - Optimized trimming of Illumina mate pair reads Changes: nxtrim (0.4.3+dfsg-3) unstable; urgency=medium . * Team upload. * Fix watch file * Standards-Version: 4.6.2 (routine-update) * Remove trailing whitespace in debian/copyright (routine-update) Checksums-Sha1: 0432c3afeaea5db89d51342c4e2acc6bdf63ca23 309736 nxtrim-dbgsym_0.4.3+dfsg-3_arm64.deb 7b5a767d79744e81bd3adcd9e08bd71ce47461ef 5139 nxtrim_0.4.3+dfsg-3_arm64.buildinfo caba708c03b88340a516f6cf473b40c3b65225f2 32688 nxtrim_0.4.3+dfsg-3_arm64.deb Checksums-Sha256: 4d073b358224e34800cdc30b218faad8a340728c48bd3ba537981cdfa66a9c6c 309736 nxtrim-dbgsym_0.4.3+dfsg-3_arm64.deb cba27eccde6a775353873278393ac3f8ca461c5afe366aca064cf0a65f99384a 5139 nxtrim_0.4.3+dfsg-3_arm64.buildinfo 9a21e4f07fedfcd1d8256763143b3e1a6d8e8aa3af8b86d55bf7d2eb50807973 32688 nxtrim_0.4.3+dfsg-3_arm64.deb Files: 69ad1546fdaf9e5c783ff07622806a07 309736 debug optional nxtrim-dbgsym_0.4.3+dfsg-3_arm64.deb 99b33ea03d7b2df6f33458b95878d178 5139 science optional nxtrim_0.4.3+dfsg-3_arm64.buildinfo 613b9b471d68ecaa735e88e4353eba80 32688 science optional nxtrim_0.4.3+dfsg-3_arm64.deb Sat May 11 12:35:48 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_22-10183.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.xKYhEMph/nxtrim_0.4.3+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.xKYhEMph/nxtrim_0.4.3+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.xKYhEMph/nxtrim_0.4.3+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.xKYhEMph/b1/nxtrim_0.4.3+dfsg-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.xKYhEMph/b2/nxtrim_0.4.3+dfsg-3_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: 0.360s) 0.359s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.019s) 0.019s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 691ms CPU time consumed: 692ms Sat May 11 12:35:50 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Sat May 11 12:35:50 UTC 2024 I: nxtrim from unstable built successfully and reproducibly on arm64. Sat May 11 12:35:51 UTC 2024 I: Submitting .buildinfo files to external archives: Sat May 11 12:35:51 UTC 2024 I: Submitting 8.0K b1/nxtrim_0.4.3+dfsg-3_arm64.buildinfo.asc Sat May 11 12:35:52 UTC 2024 I: Submitting 8.0K b2/nxtrim_0.4.3+dfsg-3_arm64.buildinfo.asc Sat May 11 12:35:53 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 11 12:35:53 UTC 2024 I: Done submitting .buildinfo files. Sat May 11 12:35:53 UTC 2024 I: Removing signed nxtrim_0.4.3+dfsg-3_arm64.buildinfo.asc files: removed './b1/nxtrim_0.4.3+dfsg-3_arm64.buildinfo.asc' removed './b2/nxtrim_0.4.3+dfsg-3_arm64.buildinfo.asc'