Mon May 13 10:24:43 UTC 2024 I: starting to build muscle3/unstable/i386 on jenkins on '2024-05-13 10:24' Mon May 13 10:24:43 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_8/27573/console.log Mon May 13 10:24:43 UTC 2024 I: Downloading source for unstable/muscle3=3.8.1551-3 --2024-05-13 10:24:43-- 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% 311M=0s 2024-05-13 10:24:43 (311 MB/s) - ‘muscle3_3.8.1551-3.dsc’ saved [2162/2162] Mon May 13 10:24:43 UTC 2024 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----- Mon May 13 10:24:43 UTC 2024 I: Checking whether the package is not for us Mon May 13 10:24:43 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Mon May 13 10:24:43 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Mon May 13 10:26:20 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 15 04:47:46 -12 2025 I: pbuilder-time-stamp: 1750006066 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job 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 gpgv: Signature made Sun Dec 17 14:09:02 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./muscle3_3.8.1551-3.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/71389/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='b83517ccef5548d68be37ea81faaa647' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='71389' 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.0KxWeshq/pbuilderrc_ixmN --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0KxWeshq/b1 --logfile b1/build.log muscle3_3.8.1551-3.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos16-i386 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 14 14:06 /bin -> usr/bin I: user script /srv/workspace/pbuilder/71389/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: i386 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 ... 19684 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} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 19.3 MB of archives. After unpacking 73.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-4 [1194 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40-8 [97.2 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 man-db i386 2.12.1-1 [1421 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.9.14+dfsg-1.3+b3 [727 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 debhelper all 13.15.3 [901 kB] Fetched 19.3 MB in 0s (63.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19684 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_i386.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_i386.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_i386.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_i386.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.7-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_i386.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../22-libelf1t64_0.191-1+b1_i386.deb ... Unpacking libelf1t64:i386 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../24-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Setting up libpipeline1:i386 (1.5.7-2) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:i386 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:i386 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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 i386 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 -j22 "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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 diaglist.cpp -o diaglist.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 diffobjscore.cpp -o diffobjscore.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 diffpaths.cpp -o diffpaths.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 difftrees.cpp -o difftrees.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 difftreese.cpp -o difftreese.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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++ cc1plus: warning: '-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++ cc1plus: warning: '-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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 distpwkimura.cpp -o distpwkimura.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 dosp.cpp -o dosp.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 drawtree.cpp -o drawtree.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 enumtostr.cpp -o enumtostr.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 fasta2.cpp -o fasta2.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 fastclust.cpp -o fastclust.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 fastdist.cpp -o fastdist.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistjones.cpp -o fastdistjones.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 fastdistkmer.cpp -o fastdistkmer.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 -Wformat -Werror=format-security -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++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 glbaligndiag.cpp -o glbaligndiag.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignle.cpp -o glbalignle.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignspn.cpp -o glbalignspn.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 glbalignss.cpp -o glbalignss.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 glbalndimer.cpp -o glbalndimer.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 globalslinux.cpp -o globalslinux.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -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++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 globalsother.cpp -o globalsother.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 gonnet.cpp -o gonnet.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweight.cpp -o henikoffweight.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 henikoffweightpb.cpp -o henikoffweightpb.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 hydro.cpp -o hydro.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 intmath.cpp -o intmath.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 main.cpp -o main.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 makerootmsab.cpp -o makerootmsab.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 maketree.cpp -o maketree.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 mpam200.cpp -o mpam200.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 msa2.cpp -o msa2.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 msf.cpp -o msf.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -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++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 muscleout.cpp -o muscleout.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 nucmx.cpp -o nucmx.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple.cpp -o nwdasimple.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 nwdasimple2.cpp -o nwdasimple2.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 nwsmall.cpp -o nwsmall.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 onexception.cpp -o onexception.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 outweights.cpp -o outweights.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 pam200mafft.cpp -o pam200mafft.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 params.cpp -o params.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 phy.cpp -o phy.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 phy2.cpp -o phy2.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 phyfromclust.cpp -o phyfromclust.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 physeq.cpp -o physeq.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 ppscore.cpp -o ppscore.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 profdb.cpp -o profdb.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 progress.cpp -o progress.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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++ g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffs.cpp -o realigndiffs.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 realigndiffse.cpp -o realigndiffse.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refine.cpp -o refine.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refinehoriz.cpp -o refinehoriz.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refinesubfams.cpp -o refinesubfams.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refinetreee.cpp -o refinetreee.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 refinevert.cpp -o refinevert.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 savebest.cpp -o savebest.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 setnewhandler.cpp -o setnewhandler.o g++ -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -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++ cc1plus: warning: '-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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 tomhydro.cpp -o tomhydro.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 treefrommsa.cpp -o treefrommsa.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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 typetostr.cpp -o typetostr.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 usage.cpp -o usage.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 -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 vtml2.cpp -o vtml2.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 -Wformat -Werror=format-security -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++ g++ -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/muscle3-3.8.1551=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -funroll-loops -Winline -DNDEBUG=1 -o muscle aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln.o alpha.o anchors.o bittraceback.o blosum62.o blosumla.o clust.o cluster.o clwwt.o color.o cons.o diaglist.o diffobjscore.o diffpaths.o difftrees.o difftreese.o distcalc.o distfunc.o distpwkimura.o domuscle.o dosp.o dpreglist.o drawtree.o edgelist.o enumopts.o enumtostr.o estring.o fasta.o fasta2.o fastclust.o fastdist.o fastdistjones.o fastdistkbit.o fastdistkmer.o fastdistmafft.o fastdistnuc.o fastscorepath2.o finddiags.o finddiagsn.o glbalign.o glbalign352.o glbaligndiag.o glbalignle.o glbalignsimple.o glbalignsp.o glbalignspn.o glbalignss.o glbalndimer.o globals.o globalslinux.o globalsosx.o globalsother.o globalswin32.o gonnet.o henikoffweight.o henikoffweightpb.o html.o hydro.o intmath.o local.o main.o makerootmsa.o makerootmsab.o maketree.o mhack.o mpam200.o msa.o msa2.o msadistkimura.o msf.o muscle.o muscleout.o nucmx.o nwdasimple.o nwdasimple2.o nwdasmall.o nwrec.o nwsmall.o objscore.o objscore2.o objscoreda.o onexception.o options.o outweights.o pam200mafft.o params.o phy.o phy2.o phy3.o phy4.o phyfromclust.o phyfromfile.o physeq.o phytofile.o posgap.o ppscore.o profdb.o profile.o profilefrommsa.o progalign.o progress.o progressivealign.o pwpath.o readmx.o realigndiffs.o realigndiffse.o refine.o refinehoriz.o refinesubfams.o refinetree.o refinetreee.o refinevert.o refinew.o savebest.o scoredist.o scoregaps.o scorehistory.o scorepp.o seq.o seqvect.o setblosumweights.o setgscweights.o setnewhandler.o spfast.o sptest.o stabilize.o subfam.o subfams.o sw.o termgaps.o textfile.o threewaywt.o tomhydro.o traceback.o tracebackopt.o tracebacksw.o treefrommsa.o typetostr.o upgma2.o usage.o validateids.o vtml2.o writescorefile.o -lm -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/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_i386.deb'. dpkg-deb: building package 'muscle3' in '../muscle3_3.8.1551-3_i386.deb'. dpkg-genbuildinfo --build=binary -O../muscle3_3.8.1551-3_i386.buildinfo dpkg-genchanges --build=binary -O../muscle3_3.8.1551-3_i386.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/71389 and its subdirectories I: Current time: Sun Jun 15 04:49:19 -12 2025 I: pbuilder-time-stamp: 1750006159 Mon May 13 10:26:21 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Mon May 13 10:26:21 UTC 2024 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Mon May 13 10:27:58 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. Mon May 13 10:27:58 UTC 2024 I: muscle3_3.8.1551-3_i386.changes: Format: 1.8 Date: Sun, 17 Dec 2023 15:04:37 +0100 Source: muscle3 Binary: muscle3 muscle3-dbgsym Architecture: i386 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: 697cc2653ca7089d51a81b20957d6e2b829bff45 750144 muscle3-dbgsym_3.8.1551-3_i386.deb eb04891dd20498e5d7733799a3eb7cc7f9a2512f 5060 muscle3_3.8.1551-3_i386.buildinfo 87b45bca16786f8555f0c0591e8e9b1cac307d13 231060 muscle3_3.8.1551-3_i386.deb Checksums-Sha256: f9c00229ce44b5fe7ba661bb9e880484c74dba41e90b3fff5c164668fe1fce33 750144 muscle3-dbgsym_3.8.1551-3_i386.deb 33baa07bc7ff0ba03dda40c52f57d42572e8c2563fc55bb60362edfd129663b1 5060 muscle3_3.8.1551-3_i386.buildinfo 559b339693cb84699cc48613c99e87f2f5fadecaf51d588e1ca6423d24135d53 231060 muscle3_3.8.1551-3_i386.deb Files: 48afbe98593a4490b989bae9f5918d06 750144 debug optional muscle3-dbgsym_3.8.1551-3_i386.deb 031c613a926fb0ccaaf616df0ddab2de 5060 science optional muscle3_3.8.1551-3_i386.buildinfo 995bcad947f42173f3a16ecae4a23551 231060 science optional muscle3_3.8.1551-3_i386.deb Mon May 13 10:28:00 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_8-27573.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.0KxWeshq/muscle3_3.8.1551-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.0KxWeshq/muscle3_3.8.1551-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.0KxWeshq/muscle3_3.8.1551-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.0KxWeshq/b1/muscle3_3.8.1551-3_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.0KxWeshq/b2/muscle3_3.8.1551-3_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.476s) 0.476s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.032s) 0.032s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 826ms CPU time consumed: 817ms Mon May 13 10:28:01 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Mon May 13 10:28:01 UTC 2024 I: muscle3 from unstable built successfully and reproducibly on i386. Mon May 13 10:28:02 UTC 2024 I: Submitting .buildinfo files to external archives: Mon May 13 10:28:02 UTC 2024 I: Submitting 8.0K b1/muscle3_3.8.1551-3_i386.buildinfo.asc Mon May 13 10:28:03 UTC 2024 I: Submitting 8.0K b2/muscle3_3.8.1551-3_i386.buildinfo.asc Mon May 13 10:28:03 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 13 10:28:03 UTC 2024 I: Done submitting .buildinfo files. Mon May 13 10:28:03 UTC 2024 I: Removing signed muscle3_3.8.1551-3_i386.buildinfo.asc files: removed './b1/muscle3_3.8.1551-3_i386.buildinfo.asc' removed './b2/muscle3_3.8.1551-3_i386.buildinfo.asc'