Fri Apr 14 06:22:58 UTC 2023 I: starting to build muscle3/bookworm/arm64 on jenkins on '2023-04-14 06:22' Fri Apr 14 06:22:58 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_18/11750/console.log Fri Apr 14 06:22:58 UTC 2023 I: Downloading source for bookworm/muscle3=3.8.1551-2 --2023-04-14 06:22:59-- http://cdn-fastly.deb.debian.org/debian/pool/main/m/muscle3/muscle3_3.8.1551-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2046 (2.0K) [text/prs.lines.tag] Saving to: ‘muscle3_3.8.1551-2.dsc’ 0K . 100% 103M=0s 2023-04-14 06:22:59 (103 MB/s) - ‘muscle3_3.8.1551-2.dsc’ saved [2046/2046] Fri Apr 14 06:22:59 UTC 2023 I: muscle3_3.8.1551-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: muscle3 Binary: muscle3 Architecture: any Version: 3.8.1551-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: https://www.drive5.com/muscle/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/muscle3 Vcs-Git: https://salsa.debian.org/med-team/muscle3.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: muscle3 deb science optional arch=any Checksums-Sha1: 9d9d56e5f064686491a3ef348cd565b1fc1ff3d3 190019 muscle3_3.8.1551.orig.tar.gz 749ec0bfb45ec4c3a992130a16a3f6305f54953b 22508 muscle3_3.8.1551-2.debian.tar.xz Checksums-Sha256: c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e 190019 muscle3_3.8.1551.orig.tar.gz 20ccd04f2227a5571432512f8d1894f753f9eb3b2b4f89fb3e2f4e0db60d7bbf 22508 muscle3_3.8.1551-2.debian.tar.xz Files: 1b7c9661f275a82d3cf708f923736bf8 190019 muscle3_3.8.1551.orig.tar.gz 2592857de79020475df4253e1c7ab27c 22508 muscle3_3.8.1551-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmOLrgMUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpEmA/+KRdyd83kIBBiOiQJN+XHWtAuGIOI ktzXgPBBTYRU8nJ8Dc/1lDLFvw9rniVhvh6mktbY/wahGeO58G2xNUEWqt8dH24A atGJ2mRyBQOaD0B15HsyHWSSqhj/bxVDtfsHW3R+AnH8uAP/kJ1OghkQBH5ttSQJ Hl22liLddKWuYC3RZVQFON5komFB+rNCQR3YYq7Yx6xceWdTBJUxQWpDlDTpaDNA hTtQs/z8gX9Hh0M+Y2kUlNbmUfjSYkKVwSVQ3H7v+kRW3RhIvTcoHz7Tkk+sKgxw z3mKKKpxtQEdMaXtiEPIsnYJoRJJ1q3YAXGUnQ9Wq+FMt149TfvE5EN0UACyAumD 07EfXnD2MYRkUZkGEF9EE4w5LMSi5z9qA37lW0xv3c/lUHNgXGZyAD7pZzdzuL3e Yqkl0uUuZKBaCannKmsSto8mlLYcagO6nGsn3zDTMC5ZMSzNDnNodWanKb4upsK9 t3oHkPpdte2dSSKhc7Eh3NGNJ2b417wAXiNwYA+FyqMu1po1m0zJ0WeYKpxLaR9Q tZtlVcr33l3mbZtMHDv5ahGMtJARFpVrjVlL7V2kXcYjmsWtQJNTcypPZvJxnwnv FX2/EUeGtLBTFCQGL2Z2d97ldANWdKVNekUWUdKVlNmieuBgXoN1XCx/m94xkl0b uMpmtsv/aCE7YM4= =zn+x -----END PGP SIGNATURE----- Fri Apr 14 06:22:59 UTC 2023 I: Checking whether the package is not for us Fri Apr 14 06:22:59 UTC 2023 I: Starting 1st build on remote node codethink13-arm64.debian.net. Fri Apr 14 06:22:59 UTC 2023 I: Preparing to do remote build '1' on codethink13-arm64.debian.net. Fri Apr 14 06:24:41 UTC 2023 I: Deleting $TMPDIR on codethink13-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 16 00:46:01 -12 2024 I: pbuilder-time-stamp: 1715863561 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 [muscle3_3.8.1551-2.dsc] I: copying [./muscle3_3.8.1551.orig.tar.gz] I: copying [./muscle3_3.8.1551-2.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Dec 3 08:13:55 2022 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./muscle3_3.8.1551-2.dsc: no acceptable signature found dpkg-source: info: extracting muscle3 in muscle3-3.8.1551 dpkg-source: info: unpacking muscle3_3.8.1551.orig.tar.gz dpkg-source: info: unpacking muscle3_3.8.1551-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_Fix_FTBFS_Hurd.patch dpkg-source: info: applying makefile.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5558/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='5558' 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.Iek6C8EW/pbuilderrc_lYuh --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.Iek6C8EW/b1 --logfile b1/build.log muscle3_3.8.1551-2.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 codethink13-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 13 04:48 /bin -> usr/bin I: user script /srv/workspace/pbuilder/5558/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) 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. 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} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 18.3 MB of archives. After unpacking 74.4 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] Fetched 18.3 MB in 1s (36.5 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) ... 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 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/muscle3-3.8.1551/ && 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 > ../muscle3_3.8.1551-2_source.changes dpkg-buildpackage: info: source package muscle3 dpkg-buildpackage: info: source version 3.8.1551-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/muscle3-3.8.1551' dh_auto_build -- 'GPP=$(CXX)' make -j8 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) make[2]: Entering directory '/build/muscle3-3.8.1551' g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpath.cpp -o aligngivenpath.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpathsw.cpp -o aligngivenpathsw.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwomsas.cpp -o aligntwomsas.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwoprofs.cpp -o aligntwoprofs.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 aln.cpp -o aln.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 alpha.cpp -o alpha.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 anchors.cpp -o anchors.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 bittraceback.cpp -o bittraceback.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 blosum62.cpp -o blosum62.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 blosumla.cpp -o blosumla.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong 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-Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 profilefrommsa.cpp -o profilefrommsa.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 progalign.cpp -o progalign.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 progress.cpp -o progress.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 progressivealign.cpp -o progressivealign.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 pwpath.cpp -o pwpath.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 readmx.cpp -o readmx.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffse.cpp -o realigndiffse.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refine.cpp -o refine.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refinehoriz.cpp -o refinehoriz.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refinesubfams.cpp -o refinesubfams.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refinetree.cpp -o refinetree.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refinetreee.cpp -o refinetreee.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refinevert.cpp -o refinevert.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refinew.cpp -o refinew.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 savebest.cpp -o savebest.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 scoredist.cpp -o scoredist.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 scoregaps.cpp -o scoregaps.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 scorehistory.cpp -o scorehistory.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 scorepp.cpp -o scorepp.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 seq.cpp -o seq.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 seqvect.cpp -o seqvect.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 setblosumweights.cpp -o setblosumweights.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 setgscweights.cpp -o setgscweights.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 setnewhandler.cpp -o setnewhandler.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 spfast.cpp -o spfast.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 sptest.cpp -o sptest.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 stabilize.cpp -o stabilize.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 subfam.cpp -o subfam.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 subfams.cpp -o subfams.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 sw.cpp -o sw.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 termgaps.cpp -o termgaps.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 textfile.cpp -o textfile.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 threewaywt.cpp -o threewaywt.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 tomhydro.cpp -o tomhydro.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 traceback.cpp -o traceback.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 tracebackopt.cpp -o tracebackopt.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 tracebacksw.cpp -o tracebacksw.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 treefrommsa.cpp -o treefrommsa.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 typetostr.cpp -o typetostr.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 upgma2.cpp -o upgma2.o typetostr.cpp: In function 'const char* SecsToStr(long unsigned int)': typetostr.cpp:13:28: warning: ':' directive writing 1 byte into a region of size between 0 and 14 [-Wformat-overflow=] 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ^ typetostr.cpp:13:22: note: directive argument in the range [0, 59] 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ^~~~~~~~~~~~~~~~~~~ typetostr.cpp:13:22: note: directive argument in the range [0, 59] typetostr.cpp:13:16: note: 'sprintf' output between 9 and 23 bytes into a destination of size 16 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 usage.cpp -o usage.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 validateids.cpp -o validateids.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 vtml2.cpp -o vtml2.o g++ -c -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 writescorefile.cpp -o writescorefile.o g++ -g -O2 -ffile-prefix-map=/build/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -lm -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/muscle3-3.8.1551' make[1]: Leaving directory '/build/muscle3-3.8.1551' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/muscle3/ debian/rules override_dh_install make[1]: Entering directory '/build/muscle3-3.8.1551' dh_install mv debian/muscle3/usr/bin/muscle debian/muscle3/usr/bin/muscle3 make[1]: Leaving directory '/build/muscle3-3.8.1551' dh_installdocs dh_installchangelogs dh_installexamples 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 'muscle3' in '../muscle3_3.8.1551-2_arm64.deb'. dpkg-deb: building package 'muscle3-dbgsym' in '../muscle3-dbgsym_3.8.1551-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../muscle3_3.8.1551-2_arm64.buildinfo dpkg-genchanges --build=binary -O../muscle3_3.8.1551-2_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/5558 and its subdirectories I: Current time: Thu May 16 00:47:40 -12 2024 I: pbuilder-time-stamp: 1715863660 Fri Apr 14 06:24:42 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink12-arm64.debian.net. Fri Apr 14 06:24:42 UTC 2023 I: Preparing to do remote build '2' on codethink12-arm64.debian.net. Fri Apr 14 06:26:51 UTC 2023 I: Deleting $TMPDIR on codethink12-arm64.debian.net. Fri Apr 14 06:26:52 UTC 2023 I: muscle3_3.8.1551-2_arm64.changes: Format: 1.8 Date: Sat, 03 Dec 2022 21:11:07 +0100 Source: muscle3 Binary: muscle3 muscle3-dbgsym Architecture: arm64 Version: 3.8.1551-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: muscle3 - multiple alignment program of protein sequences Changes: muscle3 (3.8.1551-2) unstable; urgency=medium . * Team upload. * Source-only upload. Checksums-Sha1: f4c11ebc88b0fc0eeee84670829c8b01634cfb58 801092 muscle3-dbgsym_3.8.1551-2_arm64.deb 897b524828fce2b0da7e472743e5a15b6c2fd638 5145 muscle3_3.8.1551-2_arm64.buildinfo 925b304ee0d5c53865bc6403c1f105a89e66a230 225028 muscle3_3.8.1551-2_arm64.deb Checksums-Sha256: 1e970f554a7615a35897e76a74c1601dbec55a8c98dbe6239feb87751362eb78 801092 muscle3-dbgsym_3.8.1551-2_arm64.deb 4517311e15f8a0609e2ceddfa831744c5310737a0d008aa1f08eaf93f128a97e 5145 muscle3_3.8.1551-2_arm64.buildinfo 38546d87c545991e356ee59979cf90b2ec145096db9988881edb8cbd2067b0a5 225028 muscle3_3.8.1551-2_arm64.deb Files: 7469450d861950e92ab3df5c76b39095 801092 debug optional muscle3-dbgsym_3.8.1551-2_arm64.deb a9ec153f63428ce7897dc3fa7239733b 5145 science optional muscle3_3.8.1551-2_arm64.buildinfo 1cfec98b37a9d60d06e531c573b64cca 225028 science optional muscle3_3.8.1551-2_arm64.deb Fri Apr 14 06:26:55 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.Iek6C8EW/muscle3_3.8.1551-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Iek6C8EW/muscle3_3.8.1551-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Iek6C8EW/muscle3_3.8.1551-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Iek6C8EW/b1/muscle3_3.8.1551-2_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Iek6C8EW/b2/muscle3_3.8.1551-2_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 1.687s) 1.687s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.044s) 0.044s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Fri Apr 14 06:26:57 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Fri Apr 14 06:26:57 UTC 2023 I: muscle3 from bookworm built successfully and reproducibly on arm64. Fri Apr 14 06:26:58 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Apr 14 06:26:58 UTC 2023 I: Submitting 8.0K b1/muscle3_3.8.1551-2_arm64.buildinfo.asc Fri Apr 14 06:26:59 UTC 2023 I: Submitting 8.0K b2/muscle3_3.8.1551-2_arm64.buildinfo.asc Fri Apr 14 06:27:00 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Apr 14 06:27:00 UTC 2023 I: Done submitting .buildinfo files. Fri Apr 14 06:27:00 UTC 2023 I: Removing signed muscle3_3.8.1551-2_arm64.buildinfo.asc files: removed './b1/muscle3_3.8.1551-2_arm64.buildinfo.asc' removed './b2/muscle3_3.8.1551-2_arm64.buildinfo.asc'