Running as unit: rb-build-amd64_6-25790.service ==================================================================================== Thu Nov 21 22:26:20 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_6) on jenkins, called using "ionos5-amd64 ionos11-amd64" as arguments. Thu Nov 21 22:26:20 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-RMfTv3yN" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 22:26:20 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Nov 21 22:26:20 UTC 2024 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-X933i9' Thu Nov 21 22:26:23 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Nov 21 22:26:23 UTC 2024 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-KFBgmJ' ok, let's check if muscle is building anywhere yet… ok, muscle is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of muscle in unstable on amd64 on jenkins now. 1st build will be done on ionos5-amd64.debian.net. 2nd build will be done on ionos11-amd64.debian.net. ============================================================================= Thu Nov 21 22:26:38 UTC 2024 I: starting to build muscle/unstable/amd64 on jenkins on '2024-11-21 22:26' Thu Nov 21 22:26:38 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_6/25790/console.log 1732227998 amd64 unstable muscle Thu Nov 21 22:26:38 UTC 2024 I: Downloading source for unstable/muscle=1:5.1.0-1 --2024-11-21 22:26:38-- http://deb.debian.org/debian/pool/main/m/muscle/muscle_5.1.0-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2020 (2.0K) [text/prs.lines.tag] Saving to: ‘muscle_5.1.0-1.dsc’ 0K . 100% 282M=0s 2024-11-21 22:26:38 (282 MB/s) - ‘muscle_5.1.0-1.dsc’ saved [2020/2020] --2024-11-21 22:26:38-- http://deb.debian.org/debian/pool/main/m/muscle/muscle_5.1.0-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2020 (2.0K) [text/prs.lines.tag] Saving to: ‘muscle_5.1.0-1.dsc’ 0K . 100% 282M=0s 2024-11-21 22:26:38 (282 MB/s) - ‘muscle_5.1.0-1.dsc’ saved [2020/2020] Thu Nov 21 22:26:38 UTC 2024 I: muscle_5.1.0-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: muscle Binary: muscle Architecture: any Version: 1:5.1.0-1 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/muscle Vcs-Git: https://salsa.debian.org/med-team/muscle.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), debhelper Package-List: muscle deb science optional arch=any Checksums-Sha1: 1c3932b45e1b3f21314d2d6c13927e2de32b580a 185437 muscle_5.1.0.orig.tar.gz 0bdc9bd1ebfa5ad850463e7a2335005188459415 9004 muscle_5.1.0-1.debian.tar.xz Checksums-Sha256: 2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d 185437 muscle_5.1.0.orig.tar.gz 7cf091b531f07184d31e2aeb23cf653f0580f782509f140f2847924f182dd15d 9004 muscle_5.1.0-1.debian.tar.xz Files: 32cf293ee6104e0aab36ac07b5ec951e 185437 muscle_5.1.0.orig.tar.gz aa7d5bae27ed7d3b04623968fe6c5269 9004 muscle_5.1.0-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmO/0zsRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFxZw/+OOA0d0gnCpQVTIzufBcJ5NivYrIynm2I 2swKNgdAPxcA+JRvdYF2Ry66FoVioZ8t9iMvvmPvQRxeVYzaMha7m53cuY233xj6 hxbfW6RUbybNwRm50JMtnsE1JGZxSq0gFZWCSrpMlsfr82w2n5odqUqR5twpgay/ b19pWxhoNPbgZxXyZtKwo8vOUFQu50mbb4YyEDO3915k1w+2P16+e524pkyz76SP dkeNlXtdE9kLIRwYtFbIv/5Vb/jN3CQBNTOOPWrYVnOoEXEBe+AaQTgI2m/Xuljj ixnuUYvfoq+bJjjVnqqSCmLmfnsWrK/PvmyjsRWk4UwTTfQicqF/LLyGIOKdLuTw hybkc5zpy89Tm0kP7mV7RTJhwIxqEzqu2h7IcL/66t8GXFsAISnQwd4w2h9xd6NN XVj8D6Bg4f8Dq3bTezn9UMjvVTuspJK2D9rRlPXK+vhEdNiD+vKG29XqWUXXigYk RSC2qiux3qoruZOYe4VsisYgVfpji65qVqeJC1zdvyBNOsjR2WPjq9c8+zl6syCj 6wfhT9sjm9IWtCr2IyaZ5cQkiM6n+dW+2sQU47+sJk3J429TGqUGSn4tzTUfeL4n um7lMYcmnMOGIHACrYLCYK8ODhfQM9Z6V5V1pYy5dJ2nTCe1onE6SB7imyyiUpaj YXZhWUFBrvU= =eHyS -----END PGP SIGNATURE----- Thu Nov 21 22:26:38 UTC 2024 I: Checking whether the package is not for us Thu Nov 21 22:26:38 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Thu Nov 21 22:26:38 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Thu Nov 21 22:26:39 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos5-amd64.debian.net is marked as down. Thu Nov 21 22:26:39 UTC 2024 - checking via ssh if ionos5-amd64.debian.net is up. removed '/tmp/read-only-fs-test-mlrRF7' ==================================================================================== Thu Dec 25 04:49:42 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos5-amd64, called using "1 muscle unstable /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt 1:5.1.0-1" as arguments. Thu Dec 25 04:49:42 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-eo8uLbKM" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Dec 25 04:49:42 UTC 2025 I: Downloading source for unstable/muscle=1:5.1.0-1 Reading package lists... NOTICE: 'muscle' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/muscle.git Please use: git clone https://salsa.debian.org/med-team/muscle.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 196 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (dsc) [2020 B] Get:2 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (tar) [185 kB] Get:3 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (diff) [9004 B] Fetched 196 kB in 0s (2645 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'muscle' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/muscle.git Please use: git clone https://salsa.debian.org/med-team/muscle.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 196 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (dsc) [2020 B] Get:2 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (tar) [185 kB] Get:3 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (diff) [9004 B] Fetched 196 kB in 0s (2645 kB/s) Download complete and in download only mode ============================================================================= Building muscle in unstable on amd64 on ionos5-amd64 now. Date: Thu Dec 25 04:49:42 UTC 2025 Date UTC: Thu Dec 25 04:49:42 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 24 16:49:43 -12 2025 I: pbuilder-time-stamp: 1766638183 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 [muscle_5.1.0-1.dsc] I: copying [./muscle_5.1.0.orig.tar.gz] I: copying [./muscle_5.1.0-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 12 09:30:35 2023 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 ./muscle_5.1.0-1.dsc: no acceptable signature found dpkg-source: info: extracting muscle in muscle-5.1.0 dpkg-source: info: unpacking muscle_5.1.0.orig.tar.gz dpkg-source: info: unpacking muscle_5.1.0-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2190344/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='284312b6a9f2462cb002a3d2593921fe' 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='2190344' 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.wjnBZ7Qt/pbuilderrc_JCmy --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.wjnBZ7Qt/b1 --logfile b1/build.log muscle_5.1.0-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2190344/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 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 debhelper; however: Package debhelper 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} 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, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.8 MB of archives. After unpacking 75.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Fetched 19.8 MB in 6s (3276 kB/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 ... 19966 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/muscle-5.1.0/ && 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 > ../muscle_5.1.0-1_source.changes dpkg-buildpackage: info: source package muscle dpkg-buildpackage: info: source version 1:5.1.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j42 clean make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' rm -rf gitver.txt Linux/ make[1]: Leaving directory '/build/reproducible-path/muscle-5.1.0/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0' dh_auto_build -- 'GPP=$(CXX)' cd src && make -j42 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' bash ./gitver.bash mkdir -p Linux/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/addconfseq.o addconfseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/align.o align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alignpairflat.o alignpairflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/allocflat.o allocflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnalnsflat.o alnalnsflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnmsasflat.o alnmsasflat.cpp Repo not found, git hash set to zero g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnmsasflat3.o alnmsasflat3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alpha.o alpha.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alpha3.o alpha3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/assertsameseqs.o assertsameseqs.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/buildposterior3flat.o buildposterior3flat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/buildpostflat.o buildpostflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/bwdflat3.o bwdflat3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcalnflat.o calcalnflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcalnscoreflat.o calcalnscoreflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcalnscoresparse.o calcalnscoresparse.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcposteriorflat.o calcposteriorflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/colscoreefa.o colscoreefa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/consflat.o consflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/conspairflat.o conspairflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/defaulthmmparams.o defaulthmmparams.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/derep.o derep.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/diagbox.o diagbox.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/disperse.o disperse.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/dividetree.o dividetree.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eacluster.o eacluster.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eadistmx.o eadistmx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eadistmxmsas.o eadistmxmsas.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eesort.o eesort.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efabestcols.o efabestcols.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efabestconf.o efabestconf.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efaexplode.o efaexplode.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efastats.o efastats.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/ensemble.o ensemble.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fa2efa.o fa2efa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fasta.o fasta.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fasta2.o fasta2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fwdflat3.o fwdflat3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getconsseq.o getconsseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getpairs.o getpairs.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getpostpairsalignedflat.o getpostpairsalignedflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/globalinputms.o globalinputms.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/guidetreejoinorder.o guidetreejoinorder.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/heatmapcolors.o heatmapcolors.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/help.o help.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/hmmdump.o hmmdump.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/hmmparams.o hmmparams.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/jalview.o jalview.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/jointrees.o jointrees.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/letterconf.o letterconf.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/letterconfhtml.o letterconfhtml.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/logaln.o logaln.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/logdistmx.o logdistmx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/logmx.o logmx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/main.o main.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/make_a2m.o make_a2m.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/maxcc.o maxcc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/mpcflat.o mpcflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/msa.o msa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/msa2.o msa2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/msastats.o msastats.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/multisequence.o multisequence.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/mysparsemx.o mysparsemx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/myutils.o myutils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pairhmm.o pairhmm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/permutetree.o permutetree.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/perturbhmm.o perturbhmm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog.o pprog.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog2.o pprog2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprogt.o pprogt.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/probcons.o probcons.cpp myutils.cpp:1626:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1626 | Log(" built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:1626:41: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 1626 | Log(" built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2092:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 2092 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2092:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 2092 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2115:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 2115 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2115:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 2115 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/progalnflat.o progalnflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/project.o project.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscore.o qscore.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscore2.o qscore2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscoreefa.o qscoreefa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscorer.o qscorer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/quarts.o quarts.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/randomchaintree.o randomchaintree.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/refineflat.o refineflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/relabel.o relabel.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/relaxflat.o relaxflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/resample.o resample.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/seb8.o seb8.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/seq.o seq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/sequence.o sequence.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/setprobconsparams.o setprobconsparams.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/stripgappycols.o stripgappycols.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/stripgappyrows.o stripgappyrows.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/super4.o super4.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/super5.o super5.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/testfb.o testfb.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/testlog.o testlog.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/testscoretype.o testscoretype.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/textfile.o textfile.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/totalprobflat.o totalprobflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tracebackflat.o tracebackflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/transaln.o transaln.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/transq.o transq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tree.o tree.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tree2.o tree2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tree4.o tree4.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treefromfile.o treefromfile.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treeperm.o treeperm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treesplitter.o treesplitter.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treesubsetnodes.o treesubsetnodes.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treetofile.o treetofile.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/trimtoref.o trimtoref.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/trimtorefefa.o trimtorefefa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/uclust.o uclust.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/upgma5.o upgma5.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/usage.o usage.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/usorter.o usorter.cpp g++ -Wl,-z,relro -Wl,-z,now -O3 -fopenmp -pthread -lpthread Linux/addconfseq.o Linux/align.o Linux/alignpairflat.o Linux/allocflat.o Linux/alnalnsflat.o Linux/alnmsasflat.o Linux/alnmsasflat3.o Linux/alpha.o Linux/alpha3.o Linux/assertsameseqs.o Linux/buildposterior3flat.o Linux/buildpostflat.o Linux/bwdflat3.o Linux/calcalnflat.o Linux/calcalnscoreflat.o Linux/calcalnscoresparse.o Linux/calcposteriorflat.o Linux/colscoreefa.o Linux/consflat.o Linux/conspairflat.o Linux/defaulthmmparams.o Linux/derep.o Linux/diagbox.o Linux/disperse.o Linux/dividetree.o Linux/eacluster.o Linux/eadistmx.o Linux/eadistmxmsas.o Linux/eesort.o Linux/efabestcols.o Linux/efabestconf.o Linux/efaexplode.o Linux/efastats.o Linux/ensemble.o Linux/fa2efa.o Linux/fasta.o Linux/fasta2.o Linux/fwdflat3.o Linux/getconsseq.o Linux/getpairs.o Linux/getpostpairsalignedflat.o Linux/globalinputms.o Linux/guidetreejoinorder.o Linux/heatmapcolors.o Linux/help.o Linux/hmmdump.o Linux/hmmparams.o Linux/jalview.o Linux/jointrees.o Linux/letterconf.o Linux/letterconfhtml.o Linux/logaln.o Linux/logdistmx.o Linux/logmx.o Linux/main.o Linux/make_a2m.o Linux/maxcc.o Linux/mpcflat.o Linux/msa.o Linux/msa2.o Linux/msastats.o Linux/multisequence.o Linux/mysparsemx.o Linux/myutils.o Linux/pairhmm.o Linux/permutetree.o Linux/perturbhmm.o Linux/pprog.o Linux/pprog2.o Linux/pprogt.o Linux/probcons.o Linux/progalnflat.o Linux/project.o Linux/qscore.o Linux/qscore2.o Linux/qscoreefa.o Linux/qscorer.o Linux/quarts.o Linux/randomchaintree.o Linux/refineflat.o Linux/relabel.o Linux/relaxflat.o Linux/resample.o Linux/seb8.o Linux/seq.o Linux/sequence.o Linux/setprobconsparams.o Linux/stripgappycols.o Linux/stripgappyrows.o Linux/super4.o Linux/super5.o Linux/testfb.o Linux/testlog.o Linux/testscoretype.o Linux/textfile.o Linux/totalprobflat.o Linux/tracebackflat.o Linux/transaln.o Linux/transq.o Linux/tree.o Linux/tree2.o Linux/tree4.o Linux/treefromfile.o Linux/treeperm.o Linux/treesplitter.o Linux/treesubsetnodes.o Linux/treetofile.o Linux/trimtoref.o Linux/trimtorefefa.o Linux/uclust.o Linux/upgma5.o Linux/usage.o Linux/usorter.o -o Linux/muscle # Warning: do not add -d option to strip, this is not portable #strip Linux/muscle make[2]: Leaving directory '/build/reproducible-path/muscle-5.1.0/src' make[1]: Leaving directory '/build/reproducible-path/muscle-5.1.0' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install --destdir=debian/muscle/ -O--sourcedirectory=src dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'muscle' in '../muscle_5.1.0-1_amd64.deb'. dpkg-deb: building package 'muscle-dbgsym' in '../muscle-dbgsym_5.1.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../muscle_5.1.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../muscle_5.1.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/2190344 and its subdirectories I: Current time: Wed Dec 24 16:52:07 -12 2025 I: pbuilder-time-stamp: 1766638327 Thu Dec 25 04:52:07 UTC 2025 I: Signing ./b1/muscle_5.1.0-1_amd64.buildinfo as muscle_5.1.0-1_amd64.buildinfo.asc Thu Dec 25 04:52:07 UTC 2025 I: Signed ./b1/muscle_5.1.0-1_amd64.buildinfo as ./b1/muscle_5.1.0-1_amd64.buildinfo.asc Thu Dec 25 04:52:07 UTC 2025 - build #1 for muscle/unstable/amd64 on ionos5-amd64 done. Starting cleanup. All cleanup done. Thu Dec 25 04:52:07 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-eo8uLbKM, removing. /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 22:29 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 22:26 b2 -rw-r--r-- 1 jenkins jenkins 2020 Jan 12 2023 muscle_5.1.0-1.dsc -rw------- 1 jenkins jenkins 3114 Nov 21 22:26 rbuildlog.XWDK5aW /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/b1: total 6044 -rw-r--r-- 1 jenkins jenkins 54330 Nov 21 22:29 build.log -rw-r--r-- 1 jenkins jenkins 5581348 Nov 21 22:29 muscle-dbgsym_5.1.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 9004 Nov 21 22:29 muscle_5.1.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2020 Nov 21 22:29 muscle_5.1.0-1.dsc -rw-r--r-- 1 jenkins jenkins 4946 Nov 21 22:29 muscle_5.1.0-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5828 Nov 21 22:29 muscle_5.1.0-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1539 Nov 21 22:29 muscle_5.1.0-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 317728 Nov 21 22:29 muscle_5.1.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1651 Nov 21 22:29 muscle_5.1.0-1_source.changes -rw-r--r-- 1 jenkins jenkins 185437 Nov 21 22:29 muscle_5.1.0.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/b2: total 0 Thu Nov 21 22:29:08 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 24 16:49:43 -12 2025 I: pbuilder-time-stamp: 1766638183 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 [muscle_5.1.0-1.dsc] I: copying [./muscle_5.1.0.orig.tar.gz] I: copying [./muscle_5.1.0-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 12 09:30:35 2023 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 ./muscle_5.1.0-1.dsc: no acceptable signature found dpkg-source: info: extracting muscle in muscle-5.1.0 dpkg-source: info: unpacking muscle_5.1.0.orig.tar.gz dpkg-source: info: unpacking muscle_5.1.0-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2190344/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='284312b6a9f2462cb002a3d2593921fe' 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='2190344' 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.wjnBZ7Qt/pbuilderrc_JCmy --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.wjnBZ7Qt/b1 --logfile b1/build.log muscle_5.1.0-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2190344/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 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 debhelper; however: Package debhelper 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} 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, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.8 MB of archives. After unpacking 75.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Fetched 19.8 MB in 6s (3276 kB/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 ... 19966 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.20) ... Processing triggers for libc-bin (2.40-3) ... 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/muscle-5.1.0/ && 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 > ../muscle_5.1.0-1_source.changes dpkg-buildpackage: info: source package muscle dpkg-buildpackage: info: source version 1:5.1.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j42 clean make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' rm -rf gitver.txt Linux/ make[1]: Leaving directory '/build/reproducible-path/muscle-5.1.0/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0' dh_auto_build -- 'GPP=$(CXX)' cd src && make -j42 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' bash ./gitver.bash mkdir -p Linux/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/addconfseq.o addconfseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/align.o align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alignpairflat.o alignpairflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/allocflat.o allocflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnalnsflat.o alnalnsflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnmsasflat.o alnmsasflat.cpp Repo not found, git hash set to zero g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnmsasflat3.o alnmsasflat3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alpha.o alpha.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alpha3.o alpha3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/assertsameseqs.o assertsameseqs.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/buildposterior3flat.o buildposterior3flat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/buildpostflat.o buildpostflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/bwdflat3.o bwdflat3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcalnflat.o calcalnflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcalnscoreflat.o calcalnscoreflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcalnscoresparse.o calcalnscoresparse.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcposteriorflat.o calcposteriorflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/colscoreefa.o colscoreefa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/consflat.o consflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/conspairflat.o conspairflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/defaulthmmparams.o defaulthmmparams.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/derep.o derep.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/diagbox.o diagbox.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/disperse.o disperse.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/dividetree.o dividetree.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eacluster.o eacluster.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eadistmx.o eadistmx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eadistmxmsas.o eadistmxmsas.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eesort.o eesort.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efabestcols.o efabestcols.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efabestconf.o efabestconf.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efaexplode.o efaexplode.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efastats.o efastats.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/ensemble.o ensemble.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fa2efa.o fa2efa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fasta.o fasta.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fasta2.o fasta2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fwdflat3.o fwdflat3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getconsseq.o getconsseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getpairs.o getpairs.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getpostpairsalignedflat.o getpostpairsalignedflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/globalinputms.o globalinputms.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/guidetreejoinorder.o guidetreejoinorder.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/heatmapcolors.o heatmapcolors.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/help.o help.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/hmmdump.o hmmdump.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/hmmparams.o hmmparams.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/jalview.o jalview.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/jointrees.o jointrees.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/letterconf.o letterconf.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/letterconfhtml.o letterconfhtml.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/logaln.o logaln.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/logdistmx.o logdistmx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/logmx.o logmx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/main.o main.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/make_a2m.o make_a2m.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/maxcc.o maxcc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/mpcflat.o mpcflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/msa.o msa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/msa2.o msa2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/msastats.o msastats.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/multisequence.o multisequence.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/mysparsemx.o mysparsemx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/myutils.o myutils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pairhmm.o pairhmm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/permutetree.o permutetree.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/perturbhmm.o perturbhmm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog.o pprog.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog2.o pprog2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprogt.o pprogt.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/probcons.o probcons.cpp myutils.cpp:1626:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1626 | Log(" built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:1626:41: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 1626 | Log(" built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2092:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 2092 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2092:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 2092 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2115:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 2115 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2115:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 2115 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/progalnflat.o progalnflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/project.o project.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscore.o qscore.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscore2.o qscore2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscoreefa.o qscoreefa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscorer.o qscorer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/quarts.o quarts.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/randomchaintree.o randomchaintree.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/refineflat.o refineflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/relabel.o relabel.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/relaxflat.o relaxflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/resample.o resample.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/seb8.o seb8.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/seq.o seq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/sequence.o sequence.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/setprobconsparams.o setprobconsparams.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/stripgappycols.o stripgappycols.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/stripgappyrows.o stripgappyrows.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/super4.o super4.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/super5.o super5.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/testfb.o testfb.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/testlog.o testlog.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/testscoretype.o testscoretype.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/textfile.o textfile.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/totalprobflat.o totalprobflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tracebackflat.o tracebackflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/transaln.o transaln.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/transq.o transq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tree.o tree.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tree2.o tree2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tree4.o tree4.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treefromfile.o treefromfile.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treeperm.o treeperm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treesplitter.o treesplitter.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treesubsetnodes.o treesubsetnodes.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treetofile.o treetofile.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/trimtoref.o trimtoref.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/trimtorefefa.o trimtorefefa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/uclust.o uclust.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/upgma5.o upgma5.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/usage.o usage.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/usorter.o usorter.cpp g++ -Wl,-z,relro -Wl,-z,now -O3 -fopenmp -pthread -lpthread Linux/addconfseq.o Linux/align.o Linux/alignpairflat.o Linux/allocflat.o Linux/alnalnsflat.o Linux/alnmsasflat.o Linux/alnmsasflat3.o Linux/alpha.o Linux/alpha3.o Linux/assertsameseqs.o Linux/buildposterior3flat.o Linux/buildpostflat.o Linux/bwdflat3.o Linux/calcalnflat.o Linux/calcalnscoreflat.o Linux/calcalnscoresparse.o Linux/calcposteriorflat.o Linux/colscoreefa.o Linux/consflat.o Linux/conspairflat.o Linux/defaulthmmparams.o Linux/derep.o Linux/diagbox.o Linux/disperse.o Linux/dividetree.o Linux/eacluster.o Linux/eadistmx.o Linux/eadistmxmsas.o Linux/eesort.o Linux/efabestcols.o Linux/efabestconf.o Linux/efaexplode.o Linux/efastats.o Linux/ensemble.o Linux/fa2efa.o Linux/fasta.o Linux/fasta2.o Linux/fwdflat3.o Linux/getconsseq.o Linux/getpairs.o Linux/getpostpairsalignedflat.o Linux/globalinputms.o Linux/guidetreejoinorder.o Linux/heatmapcolors.o Linux/help.o Linux/hmmdump.o Linux/hmmparams.o Linux/jalview.o Linux/jointrees.o Linux/letterconf.o Linux/letterconfhtml.o Linux/logaln.o Linux/logdistmx.o Linux/logmx.o Linux/main.o Linux/make_a2m.o Linux/maxcc.o Linux/mpcflat.o Linux/msa.o Linux/msa2.o Linux/msastats.o Linux/multisequence.o Linux/mysparsemx.o Linux/myutils.o Linux/pairhmm.o Linux/permutetree.o Linux/perturbhmm.o Linux/pprog.o Linux/pprog2.o Linux/pprogt.o Linux/probcons.o Linux/progalnflat.o Linux/project.o Linux/qscore.o Linux/qscore2.o Linux/qscoreefa.o Linux/qscorer.o Linux/quarts.o Linux/randomchaintree.o Linux/refineflat.o Linux/relabel.o Linux/relaxflat.o Linux/resample.o Linux/seb8.o Linux/seq.o Linux/sequence.o Linux/setprobconsparams.o Linux/stripgappycols.o Linux/stripgappyrows.o Linux/super4.o Linux/super5.o Linux/testfb.o Linux/testlog.o Linux/testscoretype.o Linux/textfile.o Linux/totalprobflat.o Linux/tracebackflat.o Linux/transaln.o Linux/transq.o Linux/tree.o Linux/tree2.o Linux/tree4.o Linux/treefromfile.o Linux/treeperm.o Linux/treesplitter.o Linux/treesubsetnodes.o Linux/treetofile.o Linux/trimtoref.o Linux/trimtorefefa.o Linux/uclust.o Linux/upgma5.o Linux/usage.o Linux/usorter.o -o Linux/muscle # Warning: do not add -d option to strip, this is not portable #strip Linux/muscle make[2]: Leaving directory '/build/reproducible-path/muscle-5.1.0/src' make[1]: Leaving directory '/build/reproducible-path/muscle-5.1.0' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install --destdir=debian/muscle/ -O--sourcedirectory=src dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'muscle' in '../muscle_5.1.0-1_amd64.deb'. dpkg-deb: building package 'muscle-dbgsym' in '../muscle-dbgsym_5.1.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../muscle_5.1.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../muscle_5.1.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/2190344 and its subdirectories I: Current time: Wed Dec 24 16:52:07 -12 2025 I: pbuilder-time-stamp: 1766638327 Thu Nov 21 22:29:09 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Thu Nov 21 22:29:09 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Thu Nov 21 22:29:09 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Thu Nov 21 22:29:09 UTC 2024 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-QdK03C' ==================================================================================== Thu Nov 21 22:29:10 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "2 muscle unstable /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt 1:5.1.0-1" as arguments. Thu Nov 21 22:29:10 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-E3WOcgae" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 22:29:10 UTC 2024 I: Downloading source for unstable/muscle=1:5.1.0-1 Reading package lists... NOTICE: 'muscle' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/muscle.git Please use: git clone https://salsa.debian.org/med-team/muscle.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 196 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (dsc) [2020 B] Get:2 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (tar) [185 kB] Get:3 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (diff) [9004 B] Fetched 196 kB in 0s (3256 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'muscle' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/muscle.git Please use: git clone https://salsa.debian.org/med-team/muscle.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 196 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (dsc) [2020 B] Get:2 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (tar) [185 kB] Get:3 http://deb.debian.org/debian unstable/main muscle 1:5.1.0-1 (diff) [9004 B] Fetched 196 kB in 0s (3256 kB/s) Download complete and in download only mode ============================================================================= Re-Building muscle in unstable on amd64 on ionos11-amd64 now. Date: Thu Nov 21 22:29:10 UTC 2024 Date UTC: Thu Nov 21 22:29:10 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/pbuilderrc_LUsA + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' muscle = debian-installer -o muscle = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' muscle = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/pbuilderrc_LUsA --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/b2 --logfile b2/build.log muscle_5.1.0-1.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Nov 22 12:29:10 +14 2024 I: pbuilder-time-stamp: 1732228150 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 [muscle_5.1.0-1.dsc] I: copying [./muscle_5.1.0.orig.tar.gz] I: copying [./muscle_5.1.0-1.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Jan 12 09:30:35 2023 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 ./muscle_5.1.0-1.dsc: no acceptable signature found dpkg-source: info: extracting muscle in muscle-5.1.0 dpkg-source: info: unpacking muscle_5.1.0.orig.tar.gz dpkg-source: info: unpacking muscle_5.1.0-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/503940/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Nov 21 22:29 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/503940/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/503940/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=c07502ef38c8460b849621e12f1e65b6 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=503940 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/pbuilderrc_LUsA --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/b2 --logfile b2/build.log muscle_5.1.0-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/503940/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19966 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 debhelper; however: Package debhelper 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} 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, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 19.8 MB of archives. After unpacking 75.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Fetched 19.8 MB in 1s (14.5 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 ... 19966 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.22.5-2) ... Setting up autoconf (2.72-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/503940/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/503940/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/muscle-5.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../muscle_5.1.0-1_source.changes dpkg-buildpackage: info: source package muscle dpkg-buildpackage: info: source version 1:5.1.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lance Lin dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j20 clean make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' rm -rf gitver.txt Linux/ make[1]: Leaving directory '/build/reproducible-path/muscle-5.1.0/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0' dh_auto_build -- 'GPP=$(CXX)' cd src && make -j20 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' bash ./gitver.bash mkdir -p Linux/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/addconfseq.o addconfseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/align.o align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alignpairflat.o alignpairflat.cpp Repo not found, git hash set to zero g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/allocflat.o allocflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnalnsflat.o alnalnsflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnmsasflat.o alnmsasflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnmsasflat3.o alnmsasflat3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alpha.o alpha.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alpha3.o alpha3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/assertsameseqs.o assertsameseqs.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/buildposterior3flat.o buildposterior3flat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/buildpostflat.o buildpostflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/bwdflat3.o bwdflat3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcalnflat.o calcalnflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcalnscoreflat.o calcalnscoreflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcalnscoresparse.o calcalnscoresparse.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/calcposteriorflat.o calcposteriorflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/colscoreefa.o colscoreefa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/consflat.o consflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/conspairflat.o conspairflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/defaulthmmparams.o defaulthmmparams.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/derep.o derep.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/diagbox.o diagbox.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/disperse.o disperse.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/dividetree.o dividetree.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eacluster.o eacluster.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eadistmx.o eadistmx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eadistmxmsas.o eadistmxmsas.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/eesort.o eesort.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efabestcols.o efabestcols.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efabestconf.o efabestconf.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efaexplode.o efaexplode.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/efastats.o efastats.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/ensemble.o ensemble.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fa2efa.o fa2efa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fasta.o fasta.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fasta2.o fasta2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/fwdflat3.o fwdflat3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getconsseq.o getconsseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getpairs.o getpairs.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/getpostpairsalignedflat.o getpostpairsalignedflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/globalinputms.o globalinputms.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/guidetreejoinorder.o guidetreejoinorder.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/heatmapcolors.o heatmapcolors.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/help.o help.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/hmmdump.o hmmdump.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/hmmparams.o hmmparams.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/jalview.o jalview.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/jointrees.o jointrees.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/letterconf.o letterconf.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/letterconfhtml.o letterconfhtml.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/logaln.o logaln.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/logdistmx.o logdistmx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/logmx.o logmx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/main.o main.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/make_a2m.o make_a2m.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/maxcc.o maxcc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/mpcflat.o mpcflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/msa.o msa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/msa2.o msa2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/msastats.o msastats.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/multisequence.o multisequence.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/mysparsemx.o mysparsemx.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/myutils.o myutils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pairhmm.o pairhmm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/permutetree.o permutetree.cpp myutils.cpp:1626:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1626 | Log(" built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:1626:41: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 1626 | Log(" built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2092:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 2092 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2092:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 2092 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2115:37: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 2115 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ myutils.cpp:2115:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 2115 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/perturbhmm.o perturbhmm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog.o pprog.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog2.o pprog2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprogt.o pprogt.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/probcons.o probcons.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/progalnflat.o progalnflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/project.o project.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscore.o qscore.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscore2.o qscore2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscoreefa.o qscoreefa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscorer.o qscorer.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/quarts.o quarts.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/randomchaintree.o randomchaintree.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/refineflat.o refineflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/relabel.o relabel.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/relaxflat.o relaxflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/resample.o resample.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/seb8.o seb8.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/seq.o seq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/sequence.o sequence.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/setprobconsparams.o setprobconsparams.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/stripgappycols.o stripgappycols.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/stripgappyrows.o stripgappyrows.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/super4.o super4.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/super5.o super5.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/testfb.o testfb.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/testlog.o testlog.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/testscoretype.o testscoretype.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/textfile.o textfile.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/totalprobflat.o totalprobflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tracebackflat.o tracebackflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/transaln.o transaln.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/transq.o transq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tree.o tree.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tree2.o tree2.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/tree4.o tree4.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treefromfile.o treefromfile.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treeperm.o treeperm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treesplitter.o treesplitter.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treesubsetnodes.o treesubsetnodes.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/treetofile.o treetofile.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/trimtoref.o trimtoref.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/trimtorefefa.o trimtorefefa.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/uclust.o uclust.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/upgma5.o upgma5.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/usage.o usage.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/usorter.o usorter.cpp g++ -Wl,-z,relro -Wl,-z,now -O3 -fopenmp -pthread -lpthread Linux/addconfseq.o Linux/align.o Linux/alignpairflat.o Linux/allocflat.o Linux/alnalnsflat.o Linux/alnmsasflat.o Linux/alnmsasflat3.o Linux/alpha.o Linux/alpha3.o Linux/assertsameseqs.o Linux/buildposterior3flat.o Linux/buildpostflat.o Linux/bwdflat3.o Linux/calcalnflat.o Linux/calcalnscoreflat.o Linux/calcalnscoresparse.o Linux/calcposteriorflat.o Linux/colscoreefa.o Linux/consflat.o Linux/conspairflat.o Linux/defaulthmmparams.o Linux/derep.o Linux/diagbox.o Linux/disperse.o Linux/dividetree.o Linux/eacluster.o Linux/eadistmx.o Linux/eadistmxmsas.o Linux/eesort.o Linux/efabestcols.o Linux/efabestconf.o Linux/efaexplode.o Linux/efastats.o Linux/ensemble.o Linux/fa2efa.o Linux/fasta.o Linux/fasta2.o Linux/fwdflat3.o Linux/getconsseq.o Linux/getpairs.o Linux/getpostpairsalignedflat.o Linux/globalinputms.o Linux/guidetreejoinorder.o Linux/heatmapcolors.o Linux/help.o Linux/hmmdump.o Linux/hmmparams.o Linux/jalview.o Linux/jointrees.o Linux/letterconf.o Linux/letterconfhtml.o Linux/logaln.o Linux/logdistmx.o Linux/logmx.o Linux/main.o Linux/make_a2m.o Linux/maxcc.o Linux/mpcflat.o Linux/msa.o Linux/msa2.o Linux/msastats.o Linux/multisequence.o Linux/mysparsemx.o Linux/myutils.o Linux/pairhmm.o Linux/permutetree.o Linux/perturbhmm.o Linux/pprog.o Linux/pprog2.o Linux/pprogt.o Linux/probcons.o Linux/progalnflat.o Linux/project.o Linux/qscore.o Linux/qscore2.o Linux/qscoreefa.o Linux/qscorer.o Linux/quarts.o Linux/randomchaintree.o Linux/refineflat.o Linux/relabel.o Linux/relaxflat.o Linux/resample.o Linux/seb8.o Linux/seq.o Linux/sequence.o Linux/setprobconsparams.o Linux/stripgappycols.o Linux/stripgappyrows.o Linux/super4.o Linux/super5.o Linux/testfb.o Linux/testlog.o Linux/testscoretype.o Linux/textfile.o Linux/totalprobflat.o Linux/tracebackflat.o Linux/transaln.o Linux/transq.o Linux/tree.o Linux/tree2.o Linux/tree4.o Linux/treefromfile.o Linux/treeperm.o Linux/treesplitter.o Linux/treesubsetnodes.o Linux/treetofile.o Linux/trimtoref.o Linux/trimtorefefa.o Linux/uclust.o Linux/upgma5.o Linux/usage.o Linux/usorter.o -o Linux/muscle # Warning: do not add -d option to strip, this is not portable #strip Linux/muscle make[2]: Leaving directory '/build/reproducible-path/muscle-5.1.0/src' make[1]: Leaving directory '/build/reproducible-path/muscle-5.1.0' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install --destdir=debian/muscle/ -O--sourcedirectory=src dh_install -O--sourcedirectory=src dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'muscle-dbgsym' in '../muscle-dbgsym_5.1.0-1_amd64.deb'. dpkg-deb: building package 'muscle' in '../muscle_5.1.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../muscle_5.1.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../muscle_5.1.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/503940/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/503940/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/503940 and its subdirectories I: Current time: Fri Nov 22 12:30:25 +14 2024 I: pbuilder-time-stamp: 1732228225 + false + set +x Thu Nov 21 22:30:25 UTC 2024 I: Signing ./b2/muscle_5.1.0-1_amd64.buildinfo as muscle_5.1.0-1_amd64.buildinfo.asc Thu Nov 21 22:30:25 UTC 2024 I: Signed ./b2/muscle_5.1.0-1_amd64.buildinfo as ./b2/muscle_5.1.0-1_amd64.buildinfo.asc Thu Nov 21 22:30:25 UTC 2024 - build #2 for muscle/unstable/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Thu Nov 21 22:30:25 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-E3WOcgae, removing. /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt: total 76 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 22:29 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 22:30 b2 -rw-r--r-- 1 jenkins jenkins 2020 Jan 12 2023 muscle_5.1.0-1.dsc -rw------- 1 jenkins jenkins 57732 Nov 21 22:29 rbuildlog.XWDK5aW /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/b1: total 6068 -rw-r--r-- 1 jenkins jenkins 54330 Nov 21 22:29 build.log -rw-r--r-- 1 jenkins jenkins 5581348 Nov 21 22:29 muscle-dbgsym_5.1.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 9004 Nov 21 22:29 muscle_5.1.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2020 Nov 21 22:29 muscle_5.1.0-1.dsc -rw-r--r-- 1 jenkins jenkins 4946 Nov 21 22:29 muscle_5.1.0-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5828 Nov 21 22:29 muscle_5.1.0-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1539 Nov 21 22:29 muscle_5.1.0-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 317728 Nov 21 22:29 muscle_5.1.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1651 Nov 21 22:29 muscle_5.1.0-1_source.changes -rw-r--r-- 1 jenkins jenkins 185437 Nov 21 22:29 muscle_5.1.0.orig.tar.gz /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/b2: total 6044 -rw-r--r-- 1 jenkins jenkins 56242 Nov 21 22:30 build.log -rw-r--r-- 1 jenkins jenkins 5581348 Nov 21 22:30 muscle-dbgsym_5.1.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 9004 Nov 21 22:30 muscle_5.1.0-1.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2020 Nov 21 22:30 muscle_5.1.0-1.dsc -rw-r--r-- 1 jenkins jenkins 4937 Nov 21 22:30 muscle_5.1.0-1_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 5819 Nov 21 22:30 muscle_5.1.0-1_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1539 Nov 21 22:30 muscle_5.1.0-1_amd64.changes -rw-r--r-- 1 jenkins jenkins 317728 Nov 21 22:30 muscle_5.1.0-1_amd64.deb -rw-r--r-- 1 jenkins jenkins 1651 Nov 21 22:30 muscle_5.1.0-1_source.changes -rw-r--r-- 1 jenkins jenkins 185437 Nov 21 22:30 muscle_5.1.0.orig.tar.gz Thu Nov 21 22:30:26 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Thu Nov 21 22:30:26 UTC 2024 I: muscle_5.1.0-1_amd64.changes: Format: 1.8 Date: Sat, 05 Nov 2022 19:45:38 +0100 Source: muscle Binary: muscle muscle-dbgsym Architecture: amd64 Version: 1:5.1.0-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Lance Lin Description: muscle - Multiple alignment program of protein sequences Changes: muscle (1:5.1.0-1) unstable; urgency=medium . * Team upload. . [ Charles Plessy ] * License is GPL-3 . [ Lance Lin ] * Standards-Version: 4.6.1 (routine-update) * Remove trailing whitespace in debian/control (routine-update) * d/patches/makefile.patch: Refresh patch to match new source Checksums-Sha1: b9840d30610b4a0fc26bed57847c7ae233605a27 5581348 muscle-dbgsym_5.1.0-1_amd64.deb 5eb38654e5d4cac6ab667fe7d1f1b7ae799d203d 4946 muscle_5.1.0-1_amd64.buildinfo 9401ebc018bfa01c3083971fdfa534b4201bafdb 317728 muscle_5.1.0-1_amd64.deb Checksums-Sha256: 541be3fc07ccd91362db8d8343263d0009e9ab4f2612fa82fa6fee3eb3cab6d1 5581348 muscle-dbgsym_5.1.0-1_amd64.deb f88a7468aba5fbf45dbce4c7c915a9f6df743f00e01c7f7a67a6137d21a1ffd1 4946 muscle_5.1.0-1_amd64.buildinfo cb8f69f14330e15ed9a6fdc5fdc7fbd02a99b1ec0ee43b265c226d4cc9e1be6e 317728 muscle_5.1.0-1_amd64.deb Files: d7a05ad591e991af0140d62cb8b0028d 5581348 debug optional muscle-dbgsym_5.1.0-1_amd64.deb 6125039e88d1f3815d1d11b3a081595b 4946 science optional muscle_5.1.0-1_amd64.buildinfo 02cdac8bf8b13278e85ed8511dbdcadc 317728 science optional muscle_5.1.0-1_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/muscle_5.1.0-1.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/muscle_5.1.0-1.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/muscle_5.1.0-1.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/muscle_5.1.0-1.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/muscle_5.1.0-1_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/muscle_5.1.0-1.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-21 22:29:08.310060172 +0000 +++ b2/build.log 2024-11-21 22:30:26.038556117 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Dec 24 16:49:43 -12 2025 -I: pbuilder-time-stamp: 1766638183 +I: Current time: Fri Nov 22 12:29:10 +14 2024 +I: pbuilder-time-stamp: 1732228150 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying makefile.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2190344/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/503940/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 21 22:29 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/503940/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/503940/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='284312b6a9f2462cb002a3d2593921fe' - 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='2190344' - PS1='# ' - PS2='> ' + INVOCATION_ID=c07502ef38c8460b849621e12f1e65b6 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=503940 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.wjnBZ7Qt/pbuilderrc_JCmy --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.wjnBZ7Qt/b1 --logfile b1/build.log muscle_5.1.0-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/pbuilderrc_LUsA --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/b2 --logfile b2/build.log muscle_5.1.0-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2190344/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/503940/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -140,7 +172,7 @@ Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] -Fetched 19.8 MB in 6s (3276 kB/s) +Fetched 19.8 MB in 1s (14.5 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 ... 19966 files and directories currently installed.) @@ -271,7 +303,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/muscle-5.1.0/ && 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 > ../muscle_5.1.0-1_source.changes +I: user script /srv/workspace/pbuilder/503940/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/503940/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/muscle-5.1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../muscle_5.1.0-1_source.changes dpkg-buildpackage: info: source package muscle dpkg-buildpackage: info: source version 1:5.1.0-1 dpkg-buildpackage: info: source distribution unstable @@ -281,7 +317,7 @@ debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src - cd src && make -j42 clean + cd src && make -j20 clean make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' rm -rf gitver.txt Linux/ make[1]: Leaving directory '/build/reproducible-path/muscle-5.1.0/src' @@ -295,17 +331,17 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/muscle-5.1.0' dh_auto_build -- 'GPP=$(CXX)' - cd src && make -j42 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) + cd src && make -j20 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/muscle-5.1.0/src' bash ./gitver.bash mkdir -p Linux/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/addconfseq.o addconfseq.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/align.o align.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alignpairflat.o alignpairflat.cpp +Repo not found, git hash set to zero g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/allocflat.o allocflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnalnsflat.o alnalnsflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnmsasflat.o alnmsasflat.cpp -Repo not found, git hash set to zero g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alnmsasflat3.o alnmsasflat3.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alpha.o alpha.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/alpha3.o alpha3.cpp @@ -366,11 +402,6 @@ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/myutils.o myutils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pairhmm.o pairhmm.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/permutetree.o permutetree.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/perturbhmm.o perturbhmm.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog.o pprog.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog2.o pprog2.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprogt.o pprogt.cpp -g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/probcons.o probcons.cpp myutils.cpp:1626:31: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1626 | Log(" built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ @@ -389,6 +420,11 @@ myutils.cpp:2115:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 2115 | fprintf(f, "Built %s %s\n", __DATE__, __TIME__); | ^~~~~~~~ +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/perturbhmm.o perturbhmm.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog.o pprog.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprog2.o pprog2.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/pprogt.o pprogt.cpp +g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/probcons.o probcons.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/progalnflat.o progalnflat.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/project.o project.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -ffast-math -c -o Linux/qscore.o qscore.cpp @@ -461,8 +497,8 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'muscle' in '../muscle_5.1.0-1_amd64.deb'. dpkg-deb: building package 'muscle-dbgsym' in '../muscle-dbgsym_5.1.0-1_amd64.deb'. +dpkg-deb: building package 'muscle' in '../muscle_5.1.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../muscle_5.1.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../muscle_5.1.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -470,12 +506,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/503940/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/503940/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2190344 and its subdirectories -I: Current time: Wed Dec 24 16:52:07 -12 2025 -I: pbuilder-time-stamp: 1766638327 +I: removing directory /srv/workspace/pbuilder/503940 and its subdirectories +I: Current time: Fri Nov 22 12:30:25 +14 2024 +I: pbuilder-time-stamp: 1732228225 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/muscle_5.1.0-1.diff: 77.8% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/muscle_5.1.0-1.diff.gz b2/build.log: 86.4% -- replaced with stdout Compressing the 1st log... b1/build.log: 87.1% -- replaced with stdout Thu Nov 21 22:30:27 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_muscle_unstable_amd64_1732228227 + touch /var/log/reproducible-builds/diffoscope_stamp_muscle_unstable_amd64_1732228227 + RESULT=0 + systemd-run '--description=diffoscope on muscle/1:5.1.0-1 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_6-25790 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt --run-session -c jenkins-reproducible-unstable-diffoscope-0e55f053-b77a-4b66-a837-6e7181563603 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/dbd-tmp-6IiM0fI ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/muscle_5.1.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/muscle_5.1.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/muscle_5.1.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/b1/muscle_5.1.0-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/b2/muscle_5.1.0-1_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_6-25790.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/muscle_5.1.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/muscle_5.1.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/muscle_5.1.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/b1/muscle_5.1.0-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wjnBZ7Qt/b2/muscle_5.1.0-1_amd64.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: 0.398s) 0.398s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.067s) 0.067s 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: 720ms CPU time consumed: 715ms _ _ __ ___ _ _ ___ ___| | ___ | '_ ` _ \| | | / __|/ __| |/ _ \ | | | | | | |_| \__ \ (__| | __/ |_| |_| |_|\__,_|___/\___|_|\___| Thu Nov 21 22:30:28 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Nov 21 22:30:28 UTC 2024 I: muscle from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-21 22:30:29] INFO: Starting at 2024-11-21 22:30:29.426931 [2024-11-21 22:30:29] INFO: Generating the pages of 1 package(s) [2024-11-21 22:30:29] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/muscle didn't produce a buildlog, even though it has been built. [2024-11-21 22:30:29] INFO: Finished at 2024-11-21 22:30:29.909035, took: 0:00:00.482111 Thu Nov 21 22:30:29 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/muscle.html Thu Nov 21 22:30:29 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Nov 21 22:30:30 UTC 2024 I: Submitting 8.0K b1/muscle_5.1.0-1_amd64.buildinfo.asc https://buildinfo.debian.net/5eb38654e5d4cac6ab667fe7d1f1b7ae799d203d/muscle_1:5.1.0-1_amd64 Thu Nov 21 22:30:31 UTC 2024 I: Submitting 8.0K b2/muscle_5.1.0-1_amd64.buildinfo.asc https://buildinfo.debian.net/bad259a219f9a390b9e67378ad98ab82db53f5f6/muscle_1:5.1.0-1_amd64 Thu Nov 21 22:30:32 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Nov 21 22:30:32 UTC 2024 I: Done submitting .buildinfo files. Thu Nov 21 22:30:32 UTC 2024 I: Removing signed muscle_5.1.0-1_amd64.buildinfo.asc files: removed './b1/muscle_5.1.0-1_amd64.buildinfo.asc' removed './b2/muscle_5.1.0-1_amd64.buildinfo.asc' 1732228232 amd64 unstable muscle Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/muscle_5.1.0-1.rbuild.log: 83.5% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/muscle_5.1.0-1.rbuild.log.gz [2024-11-21 22:30:32] INFO: Starting at 2024-11-21 22:30:32.833800 [2024-11-21 22:30:32] INFO: Generating the pages of 1 package(s) [2024-11-21 22:30:33] INFO: Finished at 2024-11-21 22:30:33.350533, took: 0:00:00.516739 All cleanup done. Thu Nov 21 22:30:33 UTC 2024 - total duration: 0h 4m 8s. Thu Nov 21 22:30:33 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-RMfTv3yN, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 4min 12.854s CPU time consumed: 7.370s