Thu May 23 04:48:29 UTC 2024 I: starting to build muscle/trixie/armhf on jenkins on '2024-05-23 04:48' Thu May 23 04:48:29 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_16/6269/console.log Thu May 23 04:48:29 UTC 2024 I: Downloading source for trixie/muscle=1:5.1.0-1 --2024-05-23 04:48:30-- 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% 280M=0s 2024-05-23 04:48:30 (280 MB/s) - ‘muscle_5.1.0-1.dsc’ saved [2020/2020] Thu May 23 04:48:30 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 May 23 04:48:30 UTC 2024 I: Checking whether the package is not for us Thu May 23 04:48:30 UTC 2024 I: Starting 1st build on remote node virt32b-armhf-rb.debian.net. Thu May 23 04:48:30 UTC 2024 I: Preparing to do remote build '1' on virt32b-armhf-rb.debian.net. Thu May 23 04:53:51 UTC 2024 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed May 22 16:48:36 -12 2024 I: pbuilder-time-stamp: 1716439716 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/21235/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='9188cfe9dcc943108ade13628f16ba49' 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='21235' 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.yn0GAZNu/pbuilderrc_IP00 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.yn0GAZNu/b1 --logfile b1/build.log muscle_5.1.0-1.dsc' SUDO_GID='112' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32b 6.1.0-21-armmp-lpae #1 SMP Debian 6.1.90-1 (2024-05-03) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 20 11:26 /bin -> usr/bin I: user script /srv/workspace/pbuilder/21235/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: armhf 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 ... 19446 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} libdata-optlist-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libparams-util-perl{a} libpipeline1{a} libsub-exporter-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 18.5 MB of archives. After unpacking 69.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.21-14+b1 [157 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-4 [1090 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.1-1 [85.8 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.1-1 [1375 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libparams-util-perl armhf 1.102-3 [23.0 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libsub-install-perl all 0.929-1 [10.5 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libsub-prototype-perl armhf 0.03-2+b2 [9460 B] Get: 25 http://deb.debian.org/debian trixie/main armhf libsub-override-perl all 0.11-1 [10.4 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 28 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-1+b1 [183 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-4+b1 [9070 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.21-14+b1 [1230 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf debhelper all 13.15.3 [901 kB] Fetched 18.5 MB in 1s (20.0 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 ... 19446 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_armhf.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_armhf.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.1-1_armhf.deb ... Unpacking bsdextrautils (2.40.1-1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.7-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_armhf.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../19-libparams-util-perl_1.102-3_armhf.deb ... Unpacking libparams-util-perl (1.102-3) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../20-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../21-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../22-libsub-exporter-perl_0.990-1_all.deb ... Unpacking libsub-exporter-perl (0.990-1) ... Selecting previously unselected package libsub-prototype-perl. Preparing to unpack .../23-libsub-prototype-perl_0.03-2+b2_armhf.deb ... Unpacking libsub-prototype-perl (0.03-2+b2) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../24-libsub-override-perl_0.11-1_all.deb ... Unpacking libsub-override-perl (0.11-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../25-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../26-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../27-libelf1t64_0.191-1+b1_armhf.deb ... Unpacking libelf1t64:armhf (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../28-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../29-libicu72_72.1-4+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-4+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../30-libxml2_2.9.14+dfsg-1.3+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../31-gettext_0.21-14+b1_armhf.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../32-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 .../33-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../34-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:armhf (1.5.7-2) ... Setting up libicu72:armhf (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libsub-install-perl (0.929-1) ... Setting up libelf1t64:armhf (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up libparams-util-perl (1.102-3) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up groff-base (1.23.0-4) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libsub-prototype-perl (0.03-2+b2) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libsub-override-perl (0.11-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-11) ... 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 armhf debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j3 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 -j3 "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++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/addconfseq.o addconfseq.cpp Repo not found, git hash set to zero g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/align.o align.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/alignpairflat.o alignpairflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/allocflat.o allocflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/alnalnsflat.o alnalnsflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/alnmsasflat.o alnmsasflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/alnmsasflat3.o alnmsasflat3.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/alpha.o alpha.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/alpha3.o alpha3.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/assertsameseqs.o assertsameseqs.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/buildposterior3flat.o buildposterior3flat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/buildpostflat.o buildpostflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/bwdflat3.o bwdflat3.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/calcalnflat.o calcalnflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/calcalnscoreflat.o calcalnscoreflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/calcalnscoresparse.o calcalnscoresparse.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/calcposteriorflat.o calcposteriorflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/colscoreefa.o colscoreefa.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/consflat.o consflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/conspairflat.o conspairflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/defaulthmmparams.o defaulthmmparams.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/derep.o derep.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/diagbox.o diagbox.cpp derep.cpp: In member function 'uint Derep::CalcHash(const Sequence*) const': derep.cpp:15:19: warning: conversion from 'long long unsigned int' to 'uint64' {aka 'long unsigned int'} changes value from '14695981039346656037' to '2216829733' [-Woverflow] 15 | uint64 hash = 0xcbf29ce484222325uL; | ^~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/disperse.o disperse.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/dividetree.o dividetree.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/eacluster.o eacluster.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/eadistmx.o eadistmx.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/eadistmxmsas.o eadistmxmsas.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/eesort.o eesort.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/efabestcols.o efabestcols.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/efabestconf.o efabestconf.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/efaexplode.o efaexplode.cpp In file included from /usr/include/c++/13/vector:72, from myutils.h:25, from muscle.h:21, from efabestcols.cpp:1: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void cmd_efa_bestcols()' at efabestcols.cpp:46:18: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/efastats.o efastats.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/ensemble.o ensemble.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/fa2efa.o fa2efa.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from myutils.h:32, from muscle.h:21, from efastats.cpp:1: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from myutils.h:25: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void CmpRef(const Ensemble&, const MSA&, double, std::vector&, std::vector&)' at efastats.cpp:21:15, inlined from 'void cmd_efastats()' at efastats.cpp:41:9: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void CmpRef(const Ensemble&, const MSA&, double, std::vector&, std::vector&)' at efastats.cpp:22:16, inlined from 'void cmd_efastats()' at efastats.cpp:41:9: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void cmd_efastats()' at efastats.cpp:70:16: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void cmd_efastats()' at efastats.cpp:78:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void cmd_efastats()' at efastats.cpp:78:6: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void cmd_efastats()' at efastats.cpp:87:7: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void cmd_efastats()' at efastats.cpp:87:7: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void cmd_efastats()' at efastats.cpp:88:7: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void cmd_efastats()' at efastats.cpp:88:7: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/fasta.o fasta.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from myutils.h:32, from muscle.h:21, from ensemble.cpp:1: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/fasta2.o fasta2.cpp /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/fwdflat3.o fwdflat3.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/getconsseq.o getconsseq.cpp In file included from /usr/include/c++/13/vector:72, from myutils.h:25: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Ensemble::GetTestUniqueIxs(uint, const std::set >&, std::vector&, std::vector&) const' at ensemble.cpp:915:19: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Ensemble::GetDispersion(double, double&, double&) const' at ensemble.cpp:776:16: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void Ensemble::GetDispersion(double, double&, double&) const' at ensemble.cpp:777:17: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void Ensemble::GetDispersion(double, double&, double&) const' at ensemble.cpp:780:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void Ensemble::GetDispersion(double, double&, double&) const' at ensemble.cpp:780:6: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void Ensemble::GetDispersion(double, double&, double&) const' at ensemble.cpp:781:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'void Ensemble::GetDispersion(double, double&, double&) const' at ensemble.cpp:781:6: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'double Ensemble::GetMedianConf(uint) const' at ensemble.cpp:672:18: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double Ensemble::GetMedianConf(uint) const' at ensemble.cpp:674:6: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'double Ensemble::GetMedianConf(uint) const' at ensemble.cpp:674:6: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/getpairs.o getpairs.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/getpostpairsalignedflat.o getpostpairsalignedflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/globalinputms.o globalinputms.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/guidetreejoinorder.o guidetreejoinorder.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/heatmapcolors.o heatmapcolors.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/help.o help.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/hmmdump.o hmmdump.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/hmmparams.o hmmparams.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/jalview.o jalview.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/jointrees.o jointrees.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/letterconf.o letterconf.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/letterconfhtml.o letterconfhtml.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/logaln.o logaln.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/logdistmx.o logdistmx.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/logmx.o logmx.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/main.o main.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/make_a2m.o make_a2m.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/maxcc.o maxcc.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/mpcflat.o mpcflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/msa.o msa.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/msa2.o msa2.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/msastats.o msastats.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/multisequence.o multisequence.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/mysparsemx.o mysparsemx.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/myutils.o myutils.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__); | ^~~~~~~~ myutils.cpp: In function 'void IncrementRand()': myutils.cpp:2268:32: warning: right shift count >= width of type [-Wshift-count-overflow] 2268 | g_X[4] = (uint32) (Sum >> 32); | ~~~~^~~~~ g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/pairhmm.o pairhmm.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/permutetree.o permutetree.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/perturbhmm.o perturbhmm.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/pprog.o pprog.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/pprog2.o pprog2.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/pprogt.o pprogt.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/probcons.o probcons.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/progalnflat.o progalnflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/project.o project.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/qscore.o qscore.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/qscore2.o qscore2.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/qscoreefa.o qscoreefa.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/qscorer.o qscorer.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/quarts.o quarts.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/randomchaintree.o randomchaintree.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/refineflat.o refineflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/relabel.o relabel.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/relaxflat.o relaxflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/resample.o resample.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/seb8.o seb8.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/seq.o seq.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/sequence.o sequence.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/setprobconsparams.o setprobconsparams.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/stripgappycols.o stripgappycols.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/stripgappyrows.o stripgappyrows.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/super4.o super4.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/super5.o super5.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/testfb.o testfb.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/testlog.o testlog.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/testscoretype.o testscoretype.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/textfile.o textfile.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/totalprobflat.o totalprobflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/tracebackflat.o tracebackflat.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/transaln.o transaln.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/transq.o transq.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/tree.o tree.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/tree2.o tree2.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/tree4.o tree4.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/treefromfile.o treefromfile.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/treeperm.o treeperm.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/treesplitter.o treesplitter.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/treesubsetnodes.o treesubsetnodes.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/treetofile.o treetofile.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/trimtoref.o trimtoref.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/trimtorefefa.o trimtorefefa.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/uclust.o uclust.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/upgma5.o upgma5.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -fopenmp -ffast-math -c -o Linux/usage.o usage.cpp g++ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -DNDEBUG -pthread -g -O2 -ffile-prefix-map=/build/reproducible-path/muscle-5.1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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 dpkg-shlibdeps: warning: debian/muscle/usr/bin/muscle contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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_armhf.deb'. dpkg-deb: building package 'muscle-dbgsym' in '../muscle-dbgsym_5.1.0-1_armhf.deb'. dpkg-genbuildinfo --build=binary -O../muscle_5.1.0-1_armhf.buildinfo dpkg-genchanges --build=binary -O../muscle_5.1.0-1_armhf.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/21235 and its subdirectories I: Current time: Wed May 22 16:53:35 -12 2024 I: pbuilder-time-stamp: 1716440015 Thu May 23 04:53:54 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64z-armhf-rb.debian.net. Thu May 23 04:53:54 UTC 2024 I: Preparing to do remote build '2' on virt64z-armhf-rb.debian.net. Thu May 23 05:02:21 UTC 2024 I: Deleting $TMPDIR on virt64z-armhf-rb.debian.net. Thu May 23 05:02:23 UTC 2024 I: muscle_5.1.0-1_armhf.changes: Format: 1.8 Date: Sat, 05 Nov 2022 19:45:38 +0100 Source: muscle Binary: muscle muscle-dbgsym Architecture: armhf 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: 33ea1bec6e6ad9982b56b1e76503c19282983d69 5337520 muscle-dbgsym_5.1.0-1_armhf.deb ed1d35359a76e867c7b4961eccbe09e894da08df 5118 muscle_5.1.0-1_armhf.buildinfo e4dd356ce881964f4719c0232a071961691bf98d 255108 muscle_5.1.0-1_armhf.deb Checksums-Sha256: 86a0dbc034b33af223517d0c4f95d78bcc37cfcffb1f4ab6eb4f0e92d1ff87ae 5337520 muscle-dbgsym_5.1.0-1_armhf.deb a7837da98b59af75ec196e9407b6b0cc31b8f48a2fcc1451e819d233e0fb17fd 5118 muscle_5.1.0-1_armhf.buildinfo 68f19f6f72ea49296736e27d2b4fa472e5c63f3969811c85f5744ea5699fbf34 255108 muscle_5.1.0-1_armhf.deb Files: 8b2240acf0f171c4d092954b5c849320 5337520 debug optional muscle-dbgsym_5.1.0-1_armhf.deb 6c36f30955d5efbe25f9bde2bfe48a29 5118 science optional muscle_5.1.0-1_armhf.buildinfo b4567d7f44c76727f2d7a70d4f431113 255108 science optional muscle_5.1.0-1_armhf.deb Thu May 23 05:02:24 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_16-6269.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.yn0GAZNu/muscle_5.1.0-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.yn0GAZNu/muscle_5.1.0-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.yn0GAZNu/muscle_5.1.0-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.yn0GAZNu/b1/muscle_5.1.0-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.yn0GAZNu/b2/muscle_5.1.0-1_armhf.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: 0.439s) 0.439s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.079s) 0.079s 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: 850ms CPU time consumed: 849ms Thu May 23 05:02:26 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Thu May 23 05:02:26 UTC 2024 I: muscle from trixie built successfully and reproducibly on armhf. Thu May 23 05:02:27 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 23 05:02:27 UTC 2024 I: Submitting 8.0K b1/muscle_5.1.0-1_armhf.buildinfo.asc Thu May 23 05:02:28 UTC 2024 I: Submitting 8.0K b2/muscle_5.1.0-1_armhf.buildinfo.asc Thu May 23 05:02:29 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 23 05:02:29 UTC 2024 I: Done submitting .buildinfo files. Thu May 23 05:02:29 UTC 2024 I: Removing signed muscle_5.1.0-1_armhf.buildinfo.asc files: removed './b1/muscle_5.1.0-1_armhf.buildinfo.asc' removed './b2/muscle_5.1.0-1_armhf.buildinfo.asc'