Running as unit: rb-build-amd64_29-55191.service; invocation ID: 1c607120392f4db8a2838f19d2a7ed83 ==================================================================================== Fri Sep 19 07:07:42 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_29) on jenkins, called using "ionos1-amd64 ionos15-amd64" as arguments. Fri Sep 19 07:07:42 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-ZzlHYclr" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 19 07:07:42 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Fri Sep 19 07:07:42 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-AYOnTb' Fri Sep 19 07:07:42 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Sep 19 07:07:42 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-0m3vIF' ok, let's check if muscle3 is building anywhere yet… ok, muscle3 is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of muscle3 in forky on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Fri Sep 19 07:07:56 UTC 2025 I: starting to build muscle3/forky/amd64 on jenkins on '2025-09-19 07:07' Fri Sep 19 07:07:56 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_29/55191/console.log 1758265676 amd64 forky muscle3 Fri Sep 19 07:07:56 UTC 2025 I: Downloading source for forky/muscle3=3.8.1551-3 --2025-09-19 07:07:56-- http://deb.debian.org/debian/pool/main/m/muscle3/muscle3_3.8.1551-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2162 (2.1K) [text/prs.lines.tag] Saving to: ‘muscle3_3.8.1551-3.dsc’ 0K .. 100% 19.7M=0s 2025-09-19 07:07:56 (19.7 MB/s) - ‘muscle3_3.8.1551-3.dsc’ saved [2162/2162] --2025-09-19 07:07:56-- http://deb.debian.org/debian/pool/main/m/muscle3/muscle3_3.8.1551-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2162 (2.1K) [text/prs.lines.tag] Saving to: ‘muscle3_3.8.1551-3.dsc’ 0K .. 100% 19.7M=0s 2025-09-19 07:07:56 (19.7 MB/s) - ‘muscle3_3.8.1551-3.dsc’ saved [2162/2162] Fri Sep 19 07:07:56 UTC 2025 I: muscle3_3.8.1551-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: muscle3 Binary: muscle3 Architecture: any Version: 3.8.1551-3 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: https://www.drive5.com/muscle/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/muscle3 Vcs-Git: https://salsa.debian.org/med-team/muscle3.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: muscle3 deb science optional arch=any Checksums-Sha1: 9d9d56e5f064686491a3ef348cd565b1fc1ff3d3 190019 muscle3_3.8.1551.orig.tar.gz 7332727b3f578e3eb38fa9f85483be291b671d90 22592 muscle3_3.8.1551-3.debian.tar.xz Checksums-Sha256: c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e 190019 muscle3_3.8.1551.orig.tar.gz c96423b7d6b21ef0a12a39a16348d6a47c07cb434aac7ab9148daca934bd37a7 22592 muscle3_3.8.1551-3.debian.tar.xz Files: 1b7c9661f275a82d3cf708f923736bf8 190019 muscle3_3.8.1551.orig.tar.gz bc3277acd1766f2e2ad1e7d53ddad4a5 22592 muscle3_3.8.1551-3.debian.tar.xz Dgit: 1aad73295d27d0893020aad928efa2732b7fe6bf debian archive/debian/3.8.1551-3 https://git.dgit.debian.org/muscle3 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmV/AP4UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdr0Cw/+PF2G3bxVnyoh7Mvj3Da1zANOGXgt uckJ0yRNtHWjA3uUHp6Vi/EEkm6k+UBp05VGrUlNCRqyJ2XmOYeC9HOCDN4ybaIe eaHAWE9GUfOcxE66hn1O+ifoS/GzVYmvMjlXUuQRYKX2AXQpSlda1bdzzyPGJUUb mJfDK5Wkp59qxwyqFCQ52Lu3DPJo2oUcGIN6aELU9vV3A/kGYZl9BSx996HYZEYL PECvkNG1ihFWGAC3omvfvYZVYdg8yE34f5I9Y2tL50HKDcCmK+aV2dCJqJWO8nbi XY4AuOdrrchJE67phDwp7eE/6zHjAdVXDwJV9+TShzMjSoqCpNra2Saco2QkCAs3 uWK0UukAb+jlFevxqsClMqVRRnPCY1W1eBCABMz2NMtVC7HebvDVHumz72omXdep HBfUBXxvVkTUycwfD/z98G1imvtNWEN4UcOsHh9uUlwCnyoYzDQpR0zK0ggh3rMv yzEN0mA3O6xLUCVbT4Rqzvk7iOThraClDe7Jg7RA9V2C1zTV5ZaeHT3gcv9Ux+N/ uzhJJSuikny+P6C14mGhw3aKiYRnwIDPZG4a380XiVkAphLXqVpHOf41E25LCyMR GCXsUjdJq4Zdf+wfdUNnGxjTP5qUbp3V+TFjQ2yfiJXQRUnLH1Gmrv/omZ48BbBq 5zuDomrNujQm+l0= =Mc5i -----END PGP SIGNATURE----- Fri Sep 19 07:07:56 UTC 2025 I: Checking whether the package is not for us Fri Sep 19 07:07:56 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Fri Sep 19 07:07:56 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Fri Sep 19 07:07:56 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Fri Sep 19 07:07:56 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Ek9ife' ==================================================================================== Fri Sep 19 07:07:56 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 muscle3 forky /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm 3.8.1551-3" as arguments. Fri Sep 19 07:07:56 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-JlCeMv97" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Sep 19 07:07:56 UTC 2025 I: Downloading source for forky/muscle3=3.8.1551-3 Reading package lists... NOTICE: 'muscle3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/muscle3.git Please use: git clone https://salsa.debian.org/med-team/muscle3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 215 kB of source archives. Get:1 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (dsc) [2162 B] Get:2 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (tar) [190 kB] Get:3 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (diff) [22.6 kB] Fetched 215 kB in 0s (3585 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'muscle3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/muscle3.git Please use: git clone https://salsa.debian.org/med-team/muscle3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 215 kB of source archives. Get:1 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (dsc) [2162 B] Get:2 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (tar) [190 kB] Get:3 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (diff) [22.6 kB] Fetched 215 kB in 0s (3585 kB/s) Download complete and in download only mode ============================================================================= Building muscle3 in forky on amd64 on ionos1-amd64 now. Date: Fri Sep 19 07:07:57 UTC 2025 Date UTC: Fri Sep 19 07:07:57 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: Thu Sep 18 19:07:57 -12 2025 I: pbuilder-time-stamp: 1758265677 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [muscle3_3.8.1551-3.dsc] I: copying [./muscle3_3.8.1551.orig.tar.gz] I: copying [./muscle3_3.8.1551-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./muscle3_3.8.1551-3.dsc: no acceptable signature found dpkg-source: info: extracting muscle3 in muscle3-3.8.1551 dpkg-source: info: unpacking muscle3_3.8.1551.orig.tar.gz dpkg-source: info: unpacking muscle3_3.8.1551-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_Fix_FTBFS_Hurd.patch dpkg-source: info: applying makefile.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3331623/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=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4c596f9090084dd189ea16bf7678f4d7' 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='3331623' 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.bc6elabm/pbuilderrc_Cpeu --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b1 --logfile b1/build.log muscle3_3.8.1551-3.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3331623/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) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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 11.2 MB of archives. After unpacking 42.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Fetched 11.2 MB in 6s (1841 kB/s) Preconfiguring packages ... 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 ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... 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_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... 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_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... 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_13.26_all.deb ... Unpacking debhelper (13.26) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... 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/muscle3-3.8.1551/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../muscle3_3.8.1551-3_source.changes dpkg-buildpackage: info: source package muscle3 dpkg-buildpackage: info: source version 3.8.1551-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/muscle3-3.8.1551' dh_auto_build -- 'GPP=$(CXX)' make -j40 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/muscle3-3.8.1551' g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpath.cpp -o aligngivenpath.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpathsw.cpp -o aligngivenpathsw.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwomsas.cpp -o aligntwomsas.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwoprofs.cpp -o aligntwoprofs.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aln.cpp -o aln.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 alpha.cpp -o alpha.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 anchors.cpp -o anchors.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 bittraceback.cpp -o bittraceback.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 blosum62.cpp -o blosum62.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 blosumla.cpp -o blosumla.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 clust.cpp -o clust.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 cluster.cpp -o cluster.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 clwwt.cpp -o clwwt.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 color.cpp -o color.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 cons.cpp -o cons.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diaglist.cpp -o diaglist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diffobjscore.cpp -o diffobjscore.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diffpaths.cpp -o diffpaths.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 difftrees.cpp -o difftrees.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 difftreese.cpp -o difftreese.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distcalc.cpp -o distcalc.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distfunc.cpp -o distfunc.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distpwkimura.cpp -o distpwkimura.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 domuscle.cpp -o domuscle.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 dosp.cpp -o dosp.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 dpreglist.cpp -o dpreglist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 drawtree.cpp -o drawtree.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 edgelist.cpp -o edgelist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 enumopts.cpp -o enumopts.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 enumtostr.cpp -o enumtostr.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 estring.cpp -o estring.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fasta.cpp -o fasta.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fasta2.cpp -o fasta2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastclust.cpp -o fastclust.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdist.cpp -o fastdist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistjones.cpp -o fastdistjones.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkbit.cpp -o fastdistkbit.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkmer.cpp -o fastdistkmer.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistmafft.cpp -o fastdistmafft.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistnuc.cpp -o fastdistnuc.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastscorepath2.cpp -o fastscorepath2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 finddiags.cpp -o finddiags.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 finddiagsn.cpp -o finddiagsn.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign.cpp -o glbalign.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign352.cpp -o glbalign352.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbaligndiag.cpp -o glbaligndiag.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignle.cpp -o glbalignle.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsimple.cpp -o glbalignsimple.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsp.cpp -o glbalignsp.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignspn.cpp -o glbalignspn.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignss.cpp -o glbalignss.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalndimer.cpp -o glbalndimer.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globals.cpp -o globals.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalslinux.cpp -o globalslinux.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalsosx.cpp -o globalsosx.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalsother.cpp -o globalsother.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalswin32.cpp -o globalswin32.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 gonnet.cpp -o gonnet.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweight.cpp -o henikoffweight.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweightpb.cpp -o henikoffweightpb.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 html.cpp -o html.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 hydro.cpp -o hydro.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 intmath.cpp -o intmath.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 local.cpp -o local.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 main.cpp -o main.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsa.cpp -o makerootmsa.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsab.cpp -o makerootmsab.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 maketree.cpp -o maketree.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 mhack.cpp -o mhack.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 mpam200.cpp -o mpam200.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msa.cpp -o msa.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msa2.cpp -o msa2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msadistkimura.cpp -o msadistkimura.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msf.cpp -o msf.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 muscle.cpp -o muscle.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 muscleout.cpp -o muscleout.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nucmx.cpp -o nucmx.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple.cpp -o nwdasimple.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple2.cpp -o nwdasimple2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasmall.cpp -o nwdasmall.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwrec.cpp -o nwrec.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwsmall.cpp -o nwsmall.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscore.cpp -o objscore.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscore2.cpp -o objscore2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscoreda.cpp -o objscoreda.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 onexception.cpp -o onexception.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 options.cpp -o options.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 outweights.cpp -o outweights.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 pam200mafft.cpp -o pam200mafft.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 params.cpp -o params.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy.cpp -o phy.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy2.cpp -o phy2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy3.cpp -o phy3.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy4.cpp -o phy4.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromclust.cpp -o phyfromclust.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromfile.cpp -o phyfromfile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 physeq.cpp -o physeq.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phytofile.cpp -o phytofile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 posgap.cpp -o posgap.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 ppscore.cpp -o ppscore.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profdb.cpp -o profdb.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profile.cpp -o profile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profilefrommsa.cpp -o profilefrommsa.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progalign.cpp -o progalign.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progress.cpp -o progress.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progressivealign.cpp -o progressivealign.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 pwpath.cpp -o pwpath.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 readmx.cpp -o readmx.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffse.cpp -o realigndiffse.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refine.cpp -o refine.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinehoriz.cpp -o refinehoriz.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinesubfams.cpp -o refinesubfams.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinetree.cpp -o refinetree.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinetreee.cpp -o refinetreee.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinevert.cpp -o refinevert.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinew.cpp -o refinew.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 savebest.cpp -o savebest.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scoredist.cpp -o scoredist.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scoregaps.cpp -o scoregaps.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scorehistory.cpp -o scorehistory.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scorepp.cpp -o scorepp.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 seq.cpp -o seq.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 seqvect.cpp -o seqvect.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setblosumweights.cpp -o setblosumweights.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setgscweights.cpp -o setgscweights.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setnewhandler.cpp -o setnewhandler.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 spfast.cpp -o spfast.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 sptest.cpp -o sptest.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 stabilize.cpp -o stabilize.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 subfam.cpp -o subfam.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 subfams.cpp -o subfams.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 sw.cpp -o sw.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 termgaps.cpp -o termgaps.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 textfile.cpp -o textfile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 threewaywt.cpp -o threewaywt.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tomhydro.cpp -o tomhydro.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 traceback.cpp -o traceback.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tracebackopt.cpp -o tracebackopt.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tracebacksw.cpp -o tracebacksw.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 treefrommsa.cpp -o treefrommsa.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 typetostr.cpp -o typetostr.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 upgma2.cpp -o upgma2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 usage.cpp -o usage.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 validateids.cpp -o validateids.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 vtml2.cpp -o vtml2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 writescorefile.cpp -o writescorefile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ typetostr.cpp: In function 'const char* SecsToStr(long unsigned int)': typetostr.cpp:13:28: warning: ':' directive writing 1 byte into a region of size between 0 and 14 [-Wformat-overflow=] 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ^ typetostr.cpp:13:22: note: directive argument in the range [0, 59] 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ^~~~~~~~~~~~~~~~~~~ typetostr.cpp:13:22: note: directive argument in the range [0, 59] typetostr.cpp:13:16: note: 'sprintf' output between 9 and 23 bytes into a destination of size 16 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -lm -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/muscle3-3.8.1551' make[1]: Leaving directory '/build/reproducible-path/muscle3-3.8.1551' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/muscle3/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/muscle3-3.8.1551' dh_install mv debian/muscle3/usr/bin/muscle debian/muscle3/usr/bin/muscle3 make[1]: Leaving directory '/build/reproducible-path/muscle3-3.8.1551' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'muscle3-dbgsym' in '../muscle3-dbgsym_3.8.1551-3_amd64.deb'. dpkg-deb: building package 'muscle3' in '../muscle3_3.8.1551-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../muscle3_3.8.1551-3_amd64.buildinfo dpkg-genchanges --build=binary -O../muscle3_3.8.1551-3_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: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3331623 and its subdirectories I: Current time: Thu Sep 18 19:11:49 -12 2025 I: pbuilder-time-stamp: 1758265909 Fri Sep 19 07:11:49 UTC 2025 I: Signing ./b1/muscle3_3.8.1551-3_amd64.buildinfo as muscle3_3.8.1551-3_amd64.buildinfo.asc Fri Sep 19 07:11:49 UTC 2025 I: Signed ./b1/muscle3_3.8.1551-3_amd64.buildinfo as ./b1/muscle3_3.8.1551-3_amd64.buildinfo.asc Fri Sep 19 07:11:49 UTC 2025 - build #1 for muscle3/forky/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Fri Sep 19 07:11:49 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-JlCeMv97, removing. /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 19 07:11 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 19 07:07 b2 -rw-rw-r-- 1 jenkins jenkins 2162 Dec 17 2023 muscle3_3.8.1551-3.dsc -rw------- 1 jenkins jenkins 3272 Sep 19 07:07 rbuildlog.pvTZPD0 /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b1: total 1200 -rw-r--r-- 1 jenkins jenkins 76496 Sep 19 07:11 build.log -rw-r--r-- 1 jenkins jenkins 845936 Sep 19 07:11 muscle3-dbgsym_3.8.1551-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 22592 Sep 19 07:11 muscle3_3.8.1551-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2162 Sep 19 07:11 muscle3_3.8.1551-3.dsc -rw-r--r-- 1 jenkins jenkins 4874 Sep 19 07:11 muscle3_3.8.1551-3_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5756 Sep 19 07:11 muscle3_3.8.1551-3_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1639 Sep 19 07:11 muscle3_3.8.1551-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 249656 Sep 19 07:11 muscle3_3.8.1551-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 1500 Sep 19 07:11 muscle3_3.8.1551-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b2: total 0 Fri Sep 19 07:11:51 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 18 19:07:57 -12 2025 I: pbuilder-time-stamp: 1758265677 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [muscle3_3.8.1551-3.dsc] I: copying [./muscle3_3.8.1551.orig.tar.gz] I: copying [./muscle3_3.8.1551-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./muscle3_3.8.1551-3.dsc: no acceptable signature found dpkg-source: info: extracting muscle3 in muscle3-3.8.1551 dpkg-source: info: unpacking muscle3_3.8.1551.orig.tar.gz dpkg-source: info: unpacking muscle3_3.8.1551-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_Fix_FTBFS_Hurd.patch dpkg-source: info: applying makefile.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3331623/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=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4c596f9090084dd189ea16bf7678f4d7' 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='3331623' 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.bc6elabm/pbuilderrc_Cpeu --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b1 --logfile b1/build.log muscle3_3.8.1551-3.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3331623/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) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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 11.2 MB of archives. After unpacking 42.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Fetched 11.2 MB in 6s (1841 kB/s) Preconfiguring packages ... 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 ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... 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_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... 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_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... 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_13.26_all.deb ... Unpacking debhelper (13.26) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... 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/muscle3-3.8.1551/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../muscle3_3.8.1551-3_source.changes dpkg-buildpackage: info: source package muscle3 dpkg-buildpackage: info: source version 3.8.1551-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/muscle3-3.8.1551' dh_auto_build -- 'GPP=$(CXX)' make -j40 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/muscle3-3.8.1551' g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpath.cpp -o aligngivenpath.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpathsw.cpp -o aligngivenpathsw.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwomsas.cpp -o aligntwomsas.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwoprofs.cpp -o aligntwoprofs.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aln.cpp -o aln.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 alpha.cpp -o alpha.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 anchors.cpp -o anchors.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 bittraceback.cpp -o bittraceback.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 blosum62.cpp -o blosum62.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 blosumla.cpp -o blosumla.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 clust.cpp -o clust.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 cluster.cpp -o cluster.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 clwwt.cpp -o clwwt.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 color.cpp -o color.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 cons.cpp -o cons.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diaglist.cpp -o diaglist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diffobjscore.cpp -o diffobjscore.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diffpaths.cpp -o diffpaths.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 difftrees.cpp -o difftrees.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 difftreese.cpp -o difftreese.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distcalc.cpp -o distcalc.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distfunc.cpp -o distfunc.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distpwkimura.cpp -o distpwkimura.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 domuscle.cpp -o domuscle.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 dosp.cpp -o dosp.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 dpreglist.cpp -o dpreglist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 drawtree.cpp -o drawtree.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 edgelist.cpp -o edgelist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 enumopts.cpp -o enumopts.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 enumtostr.cpp -o enumtostr.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 estring.cpp -o estring.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fasta.cpp -o fasta.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fasta2.cpp -o fasta2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastclust.cpp -o fastclust.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdist.cpp -o fastdist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistjones.cpp -o fastdistjones.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkbit.cpp -o fastdistkbit.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkmer.cpp -o fastdistkmer.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistmafft.cpp -o fastdistmafft.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistnuc.cpp -o fastdistnuc.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastscorepath2.cpp -o fastscorepath2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 finddiags.cpp -o finddiags.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 finddiagsn.cpp -o finddiagsn.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign.cpp -o glbalign.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign352.cpp -o glbalign352.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbaligndiag.cpp -o glbaligndiag.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignle.cpp -o glbalignle.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsimple.cpp -o glbalignsimple.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsp.cpp -o glbalignsp.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignspn.cpp -o glbalignspn.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignss.cpp -o glbalignss.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalndimer.cpp -o glbalndimer.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globals.cpp -o globals.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalslinux.cpp -o globalslinux.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalsosx.cpp -o globalsosx.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalsother.cpp -o globalsother.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalswin32.cpp -o globalswin32.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 gonnet.cpp -o gonnet.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweight.cpp -o henikoffweight.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweightpb.cpp -o henikoffweightpb.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 html.cpp -o html.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 hydro.cpp -o hydro.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 intmath.cpp -o intmath.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 local.cpp -o local.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 main.cpp -o main.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsa.cpp -o makerootmsa.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsab.cpp -o makerootmsab.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 maketree.cpp -o maketree.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 mhack.cpp -o mhack.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 mpam200.cpp -o mpam200.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msa.cpp -o msa.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msa2.cpp -o msa2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msadistkimura.cpp -o msadistkimura.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msf.cpp -o msf.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 muscle.cpp -o muscle.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 muscleout.cpp -o muscleout.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nucmx.cpp -o nucmx.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple.cpp -o nwdasimple.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple2.cpp -o nwdasimple2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasmall.cpp -o nwdasmall.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwrec.cpp -o nwrec.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwsmall.cpp -o nwsmall.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscore.cpp -o objscore.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscore2.cpp -o objscore2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscoreda.cpp -o objscoreda.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 onexception.cpp -o onexception.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 options.cpp -o options.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 outweights.cpp -o outweights.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 pam200mafft.cpp -o pam200mafft.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 params.cpp -o params.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy.cpp -o phy.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy2.cpp -o phy2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy3.cpp -o phy3.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy4.cpp -o phy4.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromclust.cpp -o phyfromclust.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromfile.cpp -o phyfromfile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 physeq.cpp -o physeq.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phytofile.cpp -o phytofile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 posgap.cpp -o posgap.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 ppscore.cpp -o ppscore.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profdb.cpp -o profdb.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profile.cpp -o profile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profilefrommsa.cpp -o profilefrommsa.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progalign.cpp -o progalign.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progress.cpp -o progress.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progressivealign.cpp -o progressivealign.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 pwpath.cpp -o pwpath.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 readmx.cpp -o readmx.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffse.cpp -o realigndiffse.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refine.cpp -o refine.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinehoriz.cpp -o refinehoriz.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinesubfams.cpp -o refinesubfams.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinetree.cpp -o refinetree.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinetreee.cpp -o refinetreee.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinevert.cpp -o refinevert.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinew.cpp -o refinew.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 savebest.cpp -o savebest.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scoredist.cpp -o scoredist.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scoregaps.cpp -o scoregaps.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scorehistory.cpp -o scorehistory.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scorepp.cpp -o scorepp.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 seq.cpp -o seq.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 seqvect.cpp -o seqvect.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setblosumweights.cpp -o setblosumweights.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setgscweights.cpp -o setgscweights.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setnewhandler.cpp -o setnewhandler.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 spfast.cpp -o spfast.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 sptest.cpp -o sptest.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 stabilize.cpp -o stabilize.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 subfam.cpp -o subfam.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 subfams.cpp -o subfams.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 sw.cpp -o sw.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 termgaps.cpp -o termgaps.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 textfile.cpp -o textfile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 threewaywt.cpp -o threewaywt.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tomhydro.cpp -o tomhydro.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 traceback.cpp -o traceback.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tracebackopt.cpp -o tracebackopt.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tracebacksw.cpp -o tracebacksw.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 treefrommsa.cpp -o treefrommsa.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 typetostr.cpp -o typetostr.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 upgma2.cpp -o upgma2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 usage.cpp -o usage.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 validateids.cpp -o validateids.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 vtml2.cpp -o vtml2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 writescorefile.cpp -o writescorefile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ typetostr.cpp: In function 'const char* SecsToStr(long unsigned int)': typetostr.cpp:13:28: warning: ':' directive writing 1 byte into a region of size between 0 and 14 [-Wformat-overflow=] 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ^ typetostr.cpp:13:22: note: directive argument in the range [0, 59] 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ^~~~~~~~~~~~~~~~~~~ typetostr.cpp:13:22: note: directive argument in the range [0, 59] typetostr.cpp:13:16: note: 'sprintf' output between 9 and 23 bytes into a destination of size 16 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -lm -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/muscle3-3.8.1551' make[1]: Leaving directory '/build/reproducible-path/muscle3-3.8.1551' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/muscle3/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/muscle3-3.8.1551' dh_install mv debian/muscle3/usr/bin/muscle debian/muscle3/usr/bin/muscle3 make[1]: Leaving directory '/build/reproducible-path/muscle3-3.8.1551' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'muscle3-dbgsym' in '../muscle3-dbgsym_3.8.1551-3_amd64.deb'. dpkg-deb: building package 'muscle3' in '../muscle3_3.8.1551-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../muscle3_3.8.1551-3_amd64.buildinfo dpkg-genchanges --build=binary -O../muscle3_3.8.1551-3_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: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3331623 and its subdirectories I: Current time: Thu Sep 18 19:11:49 -12 2025 I: pbuilder-time-stamp: 1758265909 Fri Sep 19 07:11:51 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Fri Sep 19 07:11:51 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Fri Sep 19 07:11:51 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Fri Sep 19 07:11:51 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-al454o' ==================================================================================== Thu Oct 22 13:34:52 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 muscle3 forky /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm 3.8.1551-3" as arguments. Thu Oct 22 13:34:52 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-PcBmFONS" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Oct 22 13:34:52 UTC 2026 I: Downloading source for forky/muscle3=3.8.1551-3 Reading package lists... NOTICE: 'muscle3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/muscle3.git Please use: git clone https://salsa.debian.org/med-team/muscle3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 215 kB of source archives. Get:1 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (dsc) [2162 B] Get:2 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (tar) [190 kB] Get:3 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (diff) [22.6 kB] Fetched 215 kB in 0s (1567 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'muscle3' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/muscle3.git Please use: git clone https://salsa.debian.org/med-team/muscle3.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 215 kB of source archives. Get:1 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (dsc) [2162 B] Get:2 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (tar) [190 kB] Get:3 http://deb.debian.org/debian forky/main muscle3 3.8.1551-3 (diff) [22.6 kB] Fetched 215 kB in 0s (1567 kB/s) Download complete and in download only mode ============================================================================= Re-Building muscle3 in forky on amd64 on ionos15-amd64 now. Date: Thu Oct 22 13:34:52 UTC 2026 Date UTC: Thu Oct 22 13:34:52 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/pbuilderrc_3DRa + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' muscle3 = debian-installer -o muscle3 = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' muscle3 = u-boot ']' + case "${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.bc6elabm/pbuilderrc_3DRa --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b2 --logfile b2/build.log muscle3_3.8.1551-3.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 Oct 23 03:34:52 +14 2026 I: pbuilder-time-stamp: 1792676092 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [muscle3_3.8.1551-3.dsc] I: copying [./muscle3_3.8.1551.orig.tar.gz] I: copying [./muscle3_3.8.1551-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./muscle3_3.8.1551-3.dsc: no acceptable signature found dpkg-source: info: extracting muscle3 in muscle3-3.8.1551 dpkg-source: info: unpacking muscle3_3.8.1551.orig.tar.gz dpkg-source: info: unpacking muscle3_3.8.1551-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_Fix_FTBFS_Hurd.patch dpkg-source: info: applying makefile.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/485583/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-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 Oct 22 13:35 /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/485583/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/485583/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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(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=42 ' DIRSTACK=() DISTRIBUTION=forky EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=8d69acc1846d4cc4b80953104413afa8 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=485583 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.bc6elabm/pbuilderrc_3DRa --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b2 --logfile b2/build.log muscle3_3.8.1551-3.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/485583/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) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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 11.2 MB of archives. After unpacking 42.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 22 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Fetched 11.2 MB in 5s (2434 kB/s) Preconfiguring packages ... 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 ... 19917 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... 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_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... 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_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../23-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... 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_13.26_all.deb ... Unpacking debhelper (13.26) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Processing triggers for libc-bin (2.41-12) ... 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: user script /srv/workspace/pbuilder/485583/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for forky I: user script /srv/workspace/pbuilder/485583/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/muscle3-3.8.1551/ && 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 > ../muscle3_3.8.1551-3_source.changes dpkg-buildpackage: info: source package muscle3 dpkg-buildpackage: info: source version 3.8.1551-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/muscle3-3.8.1551' dh_auto_build -- 'GPP=$(CXX)' make -j42 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/muscle3-3.8.1551' g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpath.cpp -o aligngivenpath.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpathsw.cpp -o aligngivenpathsw.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwomsas.cpp -o aligntwomsas.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwoprofs.cpp -o aligntwoprofs.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aln.cpp -o aln.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 alpha.cpp -o alpha.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 anchors.cpp -o anchors.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 bittraceback.cpp -o bittraceback.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 blosum62.cpp -o blosum62.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 blosumla.cpp -o blosumla.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 clust.cpp -o clust.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 cluster.cpp -o cluster.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 clwwt.cpp -o clwwt.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 color.cpp -o color.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 cons.cpp -o cons.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diaglist.cpp -o diaglist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diffobjscore.cpp -o diffobjscore.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diffpaths.cpp -o diffpaths.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 difftrees.cpp -o difftrees.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 difftreese.cpp -o difftreese.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distcalc.cpp -o distcalc.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distfunc.cpp -o distfunc.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distpwkimura.cpp -o distpwkimura.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 domuscle.cpp -o domuscle.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 dosp.cpp -o dosp.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 dpreglist.cpp -o dpreglist.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 drawtree.cpp -o drawtree.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 edgelist.cpp -o edgelist.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 enumopts.cpp -o enumopts.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 enumtostr.cpp -o enumtostr.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 estring.cpp -o estring.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fasta.cpp -o fasta.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fasta2.cpp -o fasta2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastclust.cpp -o fastclust.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdist.cpp -o fastdist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistjones.cpp -o fastdistjones.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkbit.cpp -o fastdistkbit.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkmer.cpp -o fastdistkmer.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistmafft.cpp -o fastdistmafft.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistnuc.cpp -o fastdistnuc.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastscorepath2.cpp -o fastscorepath2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 finddiags.cpp -o finddiags.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 finddiagsn.cpp -o finddiagsn.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign.cpp -o glbalign.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign352.cpp -o glbalign352.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbaligndiag.cpp -o glbaligndiag.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignle.cpp -o glbalignle.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsimple.cpp -o glbalignsimple.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsp.cpp -o glbalignsp.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignspn.cpp -o glbalignspn.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignss.cpp -o glbalignss.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalndimer.cpp -o glbalndimer.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globals.cpp -o globals.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalslinux.cpp -o globalslinux.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalsosx.cpp -o globalsosx.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalsother.cpp -o globalsother.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalswin32.cpp -o globalswin32.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 gonnet.cpp -o gonnet.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweight.cpp -o henikoffweight.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweightpb.cpp -o henikoffweightpb.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 html.cpp -o html.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 hydro.cpp -o hydro.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 intmath.cpp -o intmath.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 local.cpp -o local.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 main.cpp -o main.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsa.cpp -o makerootmsa.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsab.cpp -o makerootmsab.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 maketree.cpp -o maketree.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 mhack.cpp -o mhack.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 mpam200.cpp -o mpam200.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msa.cpp -o msa.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msa2.cpp -o msa2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msadistkimura.cpp -o msadistkimura.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msf.cpp -o msf.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 muscle.cpp -o muscle.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 muscleout.cpp -o muscleout.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nucmx.cpp -o nucmx.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple.cpp -o nwdasimple.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple2.cpp -o nwdasimple2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasmall.cpp -o nwdasmall.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwrec.cpp -o nwrec.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwsmall.cpp -o nwsmall.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscore.cpp -o objscore.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscore2.cpp -o objscore2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscoreda.cpp -o objscoreda.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 onexception.cpp -o onexception.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 options.cpp -o options.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 outweights.cpp -o outweights.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 pam200mafft.cpp -o pam200mafft.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 params.cpp -o params.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy.cpp -o phy.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy2.cpp -o phy2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy3.cpp -o phy3.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy4.cpp -o phy4.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromclust.cpp -o phyfromclust.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromfile.cpp -o phyfromfile.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 physeq.cpp -o physeq.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phytofile.cpp -o phytofile.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 posgap.cpp -o posgap.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 ppscore.cpp -o ppscore.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profdb.cpp -o profdb.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profile.cpp -o profile.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profilefrommsa.cpp -o profilefrommsa.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progalign.cpp -o progalign.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progress.cpp -o progress.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progressivealign.cpp -o progressivealign.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 pwpath.cpp -o pwpath.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 readmx.cpp -o readmx.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffse.cpp -o realigndiffse.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refine.cpp -o refine.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinehoriz.cpp -o refinehoriz.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinesubfams.cpp -o refinesubfams.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinetree.cpp -o refinetree.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinetreee.cpp -o refinetreee.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinevert.cpp -o refinevert.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinew.cpp -o refinew.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 savebest.cpp -o savebest.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scoredist.cpp -o scoredist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scoregaps.cpp -o scoregaps.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scorehistory.cpp -o scorehistory.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scorepp.cpp -o scorepp.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 seq.cpp -o seq.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 seqvect.cpp -o seqvect.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setblosumweights.cpp -o setblosumweights.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setgscweights.cpp -o setgscweights.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setnewhandler.cpp -o setnewhandler.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 spfast.cpp -o spfast.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 sptest.cpp -o sptest.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 stabilize.cpp -o stabilize.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 subfam.cpp -o subfam.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 subfams.cpp -o subfams.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 sw.cpp -o sw.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 termgaps.cpp -o termgaps.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 textfile.cpp -o textfile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 threewaywt.cpp -o threewaywt.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tomhydro.cpp -o tomhydro.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 traceback.cpp -o traceback.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tracebackopt.cpp -o tracebackopt.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tracebacksw.cpp -o tracebacksw.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 treefrommsa.cpp -o treefrommsa.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 typetostr.cpp -o typetostr.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ typetostr.cpp: In function 'const char* SecsToStr(long unsigned int)': typetostr.cpp:13:28: warning: ':' directive writing 1 byte into a region of size between 0 and 14 [-Wformat-overflow=] 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ^ typetostr.cpp:13:22: note: directive argument in the range [0, 59] 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ^~~~~~~~~~~~~~~~~~~ typetostr.cpp:13:22: note: directive argument in the range [0, 59] typetostr.cpp:13:16: note: 'sprintf' output between 9 and 23 bytes into a destination of size 16 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 upgma2.cpp -o upgma2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 usage.cpp -o usage.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 validateids.cpp -o validateids.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 vtml2.cpp -o vtml2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 writescorefile.cpp -o writescorefile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -lm -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/muscle3-3.8.1551' make[1]: Leaving directory '/build/reproducible-path/muscle3-3.8.1551' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/muscle3/ debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/muscle3-3.8.1551' dh_install mv debian/muscle3/usr/bin/muscle debian/muscle3/usr/bin/muscle3 make[1]: Leaving directory '/build/reproducible-path/muscle3-3.8.1551' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'muscle3' in '../muscle3_3.8.1551-3_amd64.deb'. dpkg-deb: building package 'muscle3-dbgsym' in '../muscle3-dbgsym_3.8.1551-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../muscle3_3.8.1551-3_amd64.buildinfo dpkg-genchanges --build=binary -O../muscle3_3.8.1551-3_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: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/485583/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/485583/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/485583 and its subdirectories I: Current time: Fri Oct 23 03:36:13 +14 2026 I: pbuilder-time-stamp: 1792676173 + false + set +x Thu Oct 22 13:36:13 UTC 2026 I: Signing ./b2/muscle3_3.8.1551-3_amd64.buildinfo as muscle3_3.8.1551-3_amd64.buildinfo.asc Thu Oct 22 13:36:13 UTC 2026 I: Signed ./b2/muscle3_3.8.1551-3_amd64.buildinfo as ./b2/muscle3_3.8.1551-3_amd64.buildinfo.asc Thu Oct 22 13:36:13 UTC 2026 - build #2 for muscle3/forky/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Thu Oct 22 13:36:13 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-PcBmFONS, removing. /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm: total 96 drwxrwxr-x 2 jenkins jenkins 4096 Sep 19 07:11 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 19 07:13 b2 -rw-rw-r-- 1 jenkins jenkins 2162 Dec 17 2023 muscle3_3.8.1551-3.dsc -rw------- 1 jenkins jenkins 80056 Sep 19 07:11 rbuildlog.pvTZPD0 /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b1: total 1212 -rw-r--r-- 1 jenkins jenkins 76496 Sep 19 07:11 build.log -rw-r--r-- 1 jenkins jenkins 845936 Sep 19 07:11 muscle3-dbgsym_3.8.1551-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 22592 Sep 19 07:11 muscle3_3.8.1551-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2162 Sep 19 07:11 muscle3_3.8.1551-3.dsc -rw-r--r-- 1 jenkins jenkins 4874 Sep 19 07:11 muscle3_3.8.1551-3_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5756 Sep 19 07:11 muscle3_3.8.1551-3_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1639 Sep 19 07:11 muscle3_3.8.1551-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 249656 Sep 19 07:11 muscle3_3.8.1551-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 1500 Sep 19 07:11 muscle3_3.8.1551-3_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b2: total 1204 -rw-rw-r-- 1 jenkins jenkins 78414 Sep 19 07:13 build.log -rw-r--r-- 1 jenkins jenkins 845936 Sep 19 07:13 muscle3-dbgsym_3.8.1551-3_amd64.deb -rw-r--r-- 1 jenkins jenkins 22592 Sep 19 07:13 muscle3_3.8.1551-3.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2162 Sep 19 07:13 muscle3_3.8.1551-3.dsc -rw-rw-r-- 1 jenkins jenkins 4874 Sep 19 07:13 muscle3_3.8.1551-3_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 5756 Sep 19 07:13 muscle3_3.8.1551-3_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1639 Sep 19 07:13 muscle3_3.8.1551-3_amd64.changes -rw-r--r-- 1 jenkins jenkins 249656 Sep 19 07:13 muscle3_3.8.1551-3_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1500 Sep 19 07:13 muscle3_3.8.1551-3_source.changes Fri Sep 19 07:13:14 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Fri Sep 19 07:13:14 UTC 2025 I: muscle3_3.8.1551-3_amd64.changes: Format: 1.8 Date: Sun, 17 Dec 2023 15:04:37 +0100 Source: muscle3 Binary: muscle3 muscle3-dbgsym Architecture: amd64 Version: 3.8.1551-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: muscle3 - multiple alignment program of protein sequences Closes: 1048044 Changes: muscle3 (3.8.1551-3) unstable; urgency=medium . * Team upload. * makefile.patch: mark forwarding not-needed. * 01_Fix_FTBFS_Hurd.patch: mark forwarding missing. * d/control: declare compliance to standards version 4.6.2. * d/s/lintian-overrides: remove now unused override. * d/clean: new: cleanup build artifacts. (Closes: #1048044) Checksums-Sha1: 0b635fbbb16c4dfe0bced5a506341f18e38c4916 845936 muscle3-dbgsym_3.8.1551-3_amd64.deb 4245b42ea73f48051cbbc0051535693a14bf476a 4874 muscle3_3.8.1551-3_amd64.buildinfo ec6330fbf83b9c34eba2bf025d0adf767244c80f 249656 muscle3_3.8.1551-3_amd64.deb Checksums-Sha256: e21f353e1c002b11627f5d85ca2c294866b9777dd613e7f5f4c404c6f3408fd2 845936 muscle3-dbgsym_3.8.1551-3_amd64.deb 3bb472ce5ccb9a359c3267eb250913e566fc9ad908cca6b27650871970452e70 4874 muscle3_3.8.1551-3_amd64.buildinfo 485809921ac5e6d25993c18c0c1e0090961d04a811d78bcf3f43a26e364074b3 249656 muscle3_3.8.1551-3_amd64.deb Files: ce3bb880bf169d89f9e642e059638270 845936 debug optional muscle3-dbgsym_3.8.1551-3_amd64.deb 68c860b04b435b80daa5567c39fbd267 4874 science optional muscle3_3.8.1551-3_amd64.buildinfo b1e3414fcbe1eea61e5aa4ee10a1fc25 249656 science optional muscle3_3.8.1551-3_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/muscle3_3.8.1551-3.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/muscle3_3.8.1551-3.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/muscle3_3.8.1551-3.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/forky/amd64/muscle3_3.8.1551-3.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/forky/amd64/muscle3_3.8.1551-3_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/muscle3_3.8.1551-3.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-19 07:11:51.002157544 +0000 +++ b2/build.log 2025-09-19 07:13:14.366265955 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Sep 18 19:07:57 -12 2025 -I: pbuilder-time-stamp: 1758265677 +I: Current time: Fri Oct 23 03:34:52 +14 2026 +I: pbuilder-time-stamp: 1792676092 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -25,53 +25,85 @@ dpkg-source: info: applying makefile.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3331623/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/485583/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Oct 22 13:35 /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/485583/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/485583/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=40 ' - DISTRIBUTION='forky' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='4c596f9090084dd189ea16bf7678f4d7' - 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='3331623' - PS1='# ' - PS2='> ' + INVOCATION_ID=8d69acc1846d4cc4b80953104413afa8 + 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=485583 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.bc6elabm/pbuilderrc_Cpeu --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b1 --logfile b1/build.log muscle3_3.8.1551-3.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.bc6elabm/pbuilderrc_3DRa --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b2 --logfile b2/build.log muscle3_3.8.1551-3.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3331623/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/485583/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -136,7 +168,7 @@ Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] -Fetched 11.2 MB in 6s (1841 kB/s) +Fetched 11.2 MB in 5s (2434 kB/s) Preconfiguring packages ... 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 ... 19917 files and directories currently installed.) @@ -267,7 +299,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/muscle3-3.8.1551/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../muscle3_3.8.1551-3_source.changes +I: user script /srv/workspace/pbuilder/485583/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/485583/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/muscle3-3.8.1551/ && 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 > ../muscle3_3.8.1551-3_source.changes dpkg-buildpackage: info: source package muscle3 dpkg-buildpackage: info: source version 3.8.1551-3 dpkg-buildpackage: info: source distribution unstable @@ -286,300 +322,291 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/muscle3-3.8.1551' dh_auto_build -- 'GPP=$(CXX)' - make -j40 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) + make -j42 "INSTALL=install --strip-program=true" GPP=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/muscle3-3.8.1551' g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpath.cpp -o aligngivenpath.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligngivenpathsw.cpp -o aligngivenpathsw.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwomsas.cpp -o aligntwomsas.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aligntwoprofs.cpp -o aligntwoprofs.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 aln.cpp -o aln.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 alpha.cpp -o alpha.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 anchors.cpp -o anchors.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 bittraceback.cpp -o bittraceback.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 blosum62.cpp -o blosum62.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 blosumla.cpp -o blosumla.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 clust.cpp -o clust.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 cluster.cpp -o cluster.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 clwwt.cpp -o clwwt.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 color.cpp -o color.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 clwwt.cpp -o clwwt.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 color.cpp -o color.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 cons.cpp -o cons.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diaglist.cpp -o diaglist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diffobjscore.cpp -o diffobjscore.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diffpaths.cpp -o diffpaths.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 diffpaths.cpp -o diffpaths.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 difftrees.cpp -o difftrees.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 difftreese.cpp -o difftreese.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distcalc.cpp -o distcalc.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distfunc.cpp -o distfunc.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distfunc.cpp -o distfunc.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 distpwkimura.cpp -o distpwkimura.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 domuscle.cpp -o domuscle.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 dosp.cpp -o dosp.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 dpreglist.cpp -o dpreglist.o +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 domuscle.cpp -o domuscle.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 dosp.cpp -o dosp.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 dpreglist.cpp -o dpreglist.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 drawtree.cpp -o drawtree.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 edgelist.cpp -o edgelist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 enumopts.cpp -o enumopts.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 edgelist.cpp -o edgelist.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 enumopts.cpp -o enumopts.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 enumtostr.cpp -o enumtostr.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 estring.cpp -o estring.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fasta.cpp -o fasta.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fasta2.cpp -o fasta2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastclust.cpp -o fastclust.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdist.cpp -o fastdist.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistjones.cpp -o fastdistjones.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkbit.cpp -o fastdistkbit.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkmer.cpp -o fastdistkmer.o +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkbit.cpp -o fastdistkbit.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkmer.cpp -o fastdistkmer.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistmafft.cpp -o fastdistmafft.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistnuc.cpp -o fastdistnuc.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistnuc.cpp -o fastdistnuc.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastscorepath2.cpp -o fastscorepath2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 fastscorepath2.cpp -o fastscorepath2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 finddiags.cpp -o finddiags.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 finddiagsn.cpp -o finddiagsn.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign.cpp -o glbalign.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign352.cpp -o glbalign352.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 finddiagsn.cpp -o finddiagsn.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign.cpp -o glbalign.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalign352.cpp -o glbalign352.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbaligndiag.cpp -o glbaligndiag.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignle.cpp -o glbalignle.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsimple.cpp -o glbalignsimple.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsp.cpp -o glbalignsp.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignspn.cpp -o glbalignspn.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsimple.cpp -o glbalignsimple.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignsp.cpp -o glbalignsp.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignspn.cpp -o glbalignspn.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignss.cpp -o glbalignss.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 glbalndimer.cpp -o glbalndimer.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globals.cpp -o globals.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalslinux.cpp -o globalslinux.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalsosx.cpp -o globalsosx.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalsother.cpp -o globalsother.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalswin32.cpp -o globalswin32.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalsother.cpp -o globalsother.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 globalswin32.cpp -o globalswin32.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 gonnet.cpp -o gonnet.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweight.cpp -o henikoffweight.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweightpb.cpp -o henikoffweightpb.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 html.cpp -o html.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 hydro.cpp -o hydro.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 intmath.cpp -o intmath.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 local.cpp -o local.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 main.cpp -o main.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsa.cpp -o makerootmsa.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsab.cpp -o makerootmsab.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsa.cpp -o makerootmsa.o +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsab.cpp -o makerootmsab.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 maketree.cpp -o maketree.o +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 mhack.cpp -o mhack.o +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 mpam200.cpp -o mpam200.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msa.cpp -o msa.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msa2.cpp -o msa2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msa2.cpp -o msa2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msadistkimura.cpp -o msadistkimura.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 msf.cpp -o msf.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 muscle.cpp -o muscle.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 muscleout.cpp -o muscleout.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nucmx.cpp -o nucmx.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple.cpp -o nwdasimple.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple.cpp -o nwdasimple.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple2.cpp -o nwdasimple2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasmall.cpp -o nwdasmall.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwrec.cpp -o nwrec.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 nwsmall.cpp -o nwsmall.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscore.cpp -o objscore.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscore2.cpp -o objscore2.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 objscoreda.cpp -o objscoreda.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 onexception.cpp -o onexception.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 options.cpp -o options.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 outweights.cpp -o outweights.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 pam200mafft.cpp -o pam200mafft.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 params.cpp -o params.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 params.cpp -o params.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy.cpp -o phy.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy2.cpp -o phy2.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy2.cpp -o phy2.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy3.cpp -o phy3.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phy4.cpp -o phy4.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromclust.cpp -o phyfromclust.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromfile.cpp -o phyfromfile.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 physeq.cpp -o physeq.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 phytofile.cpp -o phytofile.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 posgap.cpp -o posgap.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 ppscore.cpp -o ppscore.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profdb.cpp -o profdb.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profile.cpp -o profile.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 profilefrommsa.cpp -o profilefrommsa.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progalign.cpp -o progalign.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progress.cpp -o progress.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 progressivealign.cpp -o progressivealign.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 pwpath.cpp -o pwpath.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 readmx.cpp -o readmx.o +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 pwpath.cpp -o pwpath.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 readmx.cpp -o readmx.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffse.cpp -o realigndiffse.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refine.cpp -o refine.o +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinehoriz.cpp -o refinehoriz.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinesubfams.cpp -o refinesubfams.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinetree.cpp -o refinetree.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinesubfams.cpp -o refinesubfams.o +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinetree.cpp -o refinetree.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinetreee.cpp -o refinetreee.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinevert.cpp -o refinevert.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinew.cpp -o refinew.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 refinew.cpp -o refinew.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 savebest.cpp -o savebest.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scoredist.cpp -o scoredist.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scoregaps.cpp -o scoregaps.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scoregaps.cpp -o scoregaps.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scorehistory.cpp -o scorehistory.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 scorepp.cpp -o scorepp.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 seq.cpp -o seq.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 seqvect.cpp -o seqvect.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setblosumweights.cpp -o setblosumweights.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setgscweights.cpp -o setgscweights.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 setnewhandler.cpp -o setnewhandler.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 spfast.cpp -o spfast.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 spfast.cpp -o spfast.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 sptest.cpp -o sptest.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 stabilize.cpp -o stabilize.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 stabilize.cpp -o stabilize.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 subfam.cpp -o subfam.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 subfams.cpp -o subfams.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 sw.cpp -o sw.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 subfams.cpp -o subfams.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 sw.cpp -o sw.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 termgaps.cpp -o termgaps.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 termgaps.cpp -o termgaps.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 textfile.cpp -o textfile.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 threewaywt.cpp -o threewaywt.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tomhydro.cpp -o tomhydro.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 traceback.cpp -o traceback.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 traceback.cpp -o traceback.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tracebackopt.cpp -o tracebackopt.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 tracebacksw.cpp -o tracebacksw.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 treefrommsa.cpp -o treefrommsa.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 typetostr.cpp -o typetostr.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 upgma2.cpp -o upgma2.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 typetostr.cpp -o typetostr.o cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 usage.cpp -o usage.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 validateids.cpp -o validateids.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 vtml2.cpp -o vtml2.o -g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 writescorefile.cpp -o writescorefile.o -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ typetostr.cpp: In function 'const char* SecsToStr(long unsigned int)': typetostr.cpp:13:28: warning: ':' directive writing 1 byte into a region of size between 0 and 14 [-Wformat-overflow=] @@ -592,6 +619,15 @@ typetostr.cpp:13:16: note: 'sprintf' output between 9 and 23 bytes into a destination of size 16 13 | sprintf(Str, "%02ld:%02ld:%02ld", hh, mm, ss); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 upgma2.cpp -o upgma2.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 usage.cpp -o usage.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 validateids.cpp -o validateids.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 vtml2.cpp -o vtml2.o +g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 writescorefile.cpp -o writescorefile.o +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -Winline -DNDEBUG=1 -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -lm -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/reproducible-path/muscle3-3.8.1551' @@ -623,8 +659,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'muscle3-dbgsym' in '../muscle3-dbgsym_3.8.1551-3_amd64.deb'. dpkg-deb: building package 'muscle3' in '../muscle3_3.8.1551-3_amd64.deb'. +dpkg-deb: building package 'muscle3-dbgsym' in '../muscle3-dbgsym_3.8.1551-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../muscle3_3.8.1551-3_amd64.buildinfo dpkg-genchanges --build=binary -O../muscle3_3.8.1551-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -632,12 +668,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/485583/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/485583/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/3331623 and its subdirectories -I: Current time: Thu Sep 18 19:11:49 -12 2025 -I: pbuilder-time-stamp: 1758265909 +I: removing directory /srv/workspace/pbuilder/485583 and its subdirectories +I: Current time: Fri Oct 23 03:36:13 +14 2026 +I: pbuilder-time-stamp: 1792676173 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/muscle3_3.8.1551-3.diff: 92.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/forky/amd64/muscle3_3.8.1551-3.diff.gz b2/build.log: 89.6% -- replaced with stdout Compressing the 1st log... b1/build.log: 90.2% -- replaced with stdout Fri Sep 19 07:13:15 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_muscle3_forky_amd64_1758265995 + touch /var/log/reproducible-builds/diffoscope_stamp_muscle3_forky_amd64_1758265995 + RESULT=0 + systemd-run '--description=diffoscope on muscle3/3.8.1551-3 in forky/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_29-55191 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm --run-session -c jenkins-reproducible-forky-diffoscope-29d097ef-5c74-492b-8274-faf97f03c675 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/dbd-tmp-07vaA7P ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/muscle3_3.8.1551-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/muscle3_3.8.1551-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/muscle3_3.8.1551-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b1/muscle3_3.8.1551-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b2/muscle3_3.8.1551-3_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_29-55191.service; invocation ID: 6c48429a3c774d79bd06a3e3ff3a119b # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/muscle3_3.8.1551-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/muscle3_3.8.1551-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/muscle3_3.8.1551-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b1/muscle3_3.8.1551-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bc6elabm/b2/muscle3_3.8.1551-3_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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 185ms CPU time consumed: 167ms Memory peak: 17.7M (swap: 0B) _ _____ _ __ ___ _ _ ___ ___| | ___|___ / | '_ ` _ \| | | / __|/ __| |/ _ \ |_ \ | | | | | | |_| \__ \ (__| | __/___) | |_| |_| |_|\__,_|___/\___|_|\___|____/ Fri Sep 19 07:13:15 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Fri Sep 19 07:13:15 UTC 2025 I: muscle3 from forky built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-19 07:13:16] INFO: Starting at 2025-09-19 07:13:16.269057 [2025-09-19 07:13:16] INFO: Generating the pages of 1 package(s) [2025-09-19 07:13:16] CRITICAL: https://tests.reproducible-builds.org/debian/forky/amd64/muscle3 didn't produce a buildlog, even though it has been built. [2025-09-19 07:13:16] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/muscle3 didn't produce a buildlog, even though it has been built. [2025-09-19 07:13:16] INFO: Finished at 2025-09-19 07:13:16.478452, took: 0:00:00.209398 Fri Sep 19 07:13:16 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/forky/amd64/muscle3.html Fri Sep 19 07:13:16 UTC 2025 I: Removing signed muscle3_3.8.1551-3_amd64.buildinfo.asc files: removed './b1/muscle3_3.8.1551-3_amd64.buildinfo.asc' removed './b2/muscle3_3.8.1551-3_amd64.buildinfo.asc' 1758265996 amd64 forky muscle3 Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/muscle3_3.8.1551-3.rbuild.log: 87.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/forky/amd64/muscle3_3.8.1551-3.rbuild.log.gz [2025-09-19 07:13:16] INFO: Starting at 2025-09-19 07:13:16.795457 [2025-09-19 07:13:16] INFO: Generating the pages of 1 package(s) [2025-09-19 07:13:16] CRITICAL: https://tests.reproducible-builds.org/debian/forky/arm64/muscle3 didn't produce a buildlog, even though it has been built. [2025-09-19 07:13:17] INFO: Finished at 2025-09-19 07:13:17.004152, took: 0:00:00.208698 All cleanup done. Fri Sep 19 07:13:17 UTC 2025 - total duration: 0h 5m 33s. Fri Sep 19 07:13:17 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-ZzlHYclr, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 5min 34.864s CPU time consumed: 3.007s Memory peak: 41.3M (swap: 0B)