Sat Jan 18 08:45:41 UTC 2025 I: starting to build fsa/trixie/arm64 on jenkins on '2025-01-18 08:45' Sat Jan 18 08:45:41 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_16/45306/console.log Sat Jan 18 08:45:41 UTC 2025 I: Downloading source for trixie/fsa=1.15.9+dfsg-6 --2025-01-18 08:45:42-- http://deb.debian.org/debian/pool/main/f/fsa/fsa_1.15.9%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1971 (1.9K) [text/prs.lines.tag] Saving to: ‘fsa_1.15.9+dfsg-6.dsc’ 0K . 100% 301M=0s 2025-01-18 08:45:42 (301 MB/s) - ‘fsa_1.15.9+dfsg-6.dsc’ saved [1971/1971] Sat Jan 18 08:45:42 UTC 2025 I: fsa_1.15.9+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: fsa Binary: fsa Architecture: any Version: 1.15.9+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://fsa.sourceforge.net/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/fsa Vcs-Git: https://salsa.debian.org/med-team/fsa.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), mummer, exonerate, help2man Package-List: fsa deb science optional arch=any Checksums-Sha1: bff4c2f27d54db9891d70e2e314bafecf801cabb 558688 fsa_1.15.9+dfsg.orig.tar.xz 2116b756b7959867ce6ceb71a6d40c6acf9b459e 13444 fsa_1.15.9+dfsg-6.debian.tar.xz Checksums-Sha256: c3a845122e08f5e3c0fb96ef5133270a386c4ac6198856fc56aa2a796c0a6377 558688 fsa_1.15.9+dfsg.orig.tar.xz 5c2cbb013a79debd8c1ca15e9cf3f9b76ad8f171e76b326a9e70823fd36cff37 13444 fsa_1.15.9+dfsg-6.debian.tar.xz Files: 8d6b1b18195dc5262113b1d363de88bf 558688 fsa_1.15.9+dfsg.orig.tar.xz b3b6cac1bebbb24ce81be6891155f3bc 13444 fsa_1.15.9+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+xYDYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE2aA//WlYn1kr0gp4xWVFytdACx6kvqmiEdStg sHIKciMkegewKTBdInLZ58tckLKWO8r+2W8FOEujrElAc+UXbzBKNg0HySHXHhM2 thUttzpZz2yREAI5Skl70FDrKPcCT36swjJbXWZRddLd7bYTnnPBAVv6KWa/U8aw B7f2d8RP9BGxdzu5HckPSHq/U4kzy0gjS9ywP4O+LKEx5SNiTzufLxjSXMNZE/ah tuCWgy/vxTTZt6iTRyEANwV2bnznvXyLa2HT2/GWuztLXICptqaNsL/qm9G/w0AL oCC8OcO0kbMBw03TUKSr0ASM6uMPGNwFtubVHeV0tRRRiuJaVqdgtwFGnmfpA8pK 4YrkltuKRt8d4H1CogTksxWVmyb/2TPG/QRwiX9UYJaTZRRVCKL1sPBJm6AMkVmt qNOs3REsLMdEezAV0wWWEDTJJBlyNKO6pLGCLcakgkd85t+AUg7iZIa+iRtL4xxX JtYSlkILVw0xVHWr8O+c2MsOMGpOBhWJKOTs0l54IFwszyLyk1F8s/b0CcNZrA45 t0XYBYEUTuC1z+K44ECzvtOxZLdgvpznJ1pDbBHmDlixI10m4xxQx8RXKEHVl11e jqRCsuLP6u+fehNQqn6X/vhtay8TtKxlYMz5ts47y4HBBO4F0j2/JvzgHR0QPcb3 YbYYMtXghso= =Zh/E -----END PGP SIGNATURE----- Sat Jan 18 08:45:42 UTC 2025 I: Checking whether the package is not for us Sat Jan 18 08:45:42 UTC 2025 I: Starting 1st build on remote node codethink02-arm64.debian.net. Sat Jan 18 08:45:42 UTC 2025 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Sat Jan 18 08:47:45 UTC 2025 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Jan 17 20:45:44 -12 2025 I: pbuilder-time-stamp: 1737189944 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [fsa_1.15.9+dfsg-6.dsc] I: copying [./fsa_1.15.9+dfsg.orig.tar.xz] I: copying [./fsa_1.15.9+dfsg-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./fsa_1.15.9+dfsg-6.dsc: unsupported subcommand dpkg-source: info: extracting fsa in fsa-1.15.9+dfsg dpkg-source: info: unpacking fsa_1.15.9+dfsg.orig.tar.xz dpkg-source: info: unpacking fsa_1.15.9+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-display.patch dpkg-source: info: applying removed-pdf-only-docs.patch dpkg-source: info: applying privacy_breach_logo.patch dpkg-source: info: applying fixed-check-for-m64-flag.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2038800/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='d63f772ac6a743abb70a8ecfa789bd8f' 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='2038800' 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.lfnEWkho/pbuilderrc_xwad --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lfnEWkho/b1 --logfile b1/build.log fsa_1.15.9+dfsg-6.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2038800/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), mummer, exonerate, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19967 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on exonerate; however: Package exonerate is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man 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} exonerate{a} file{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libffi8{a} libfile-stripnondeterminism-perl{a} libglib2.0-0t64{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libreadline8t64{a} libsigsegv2{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} mummer{a} po-debconf{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 40 newly installed, 0 to remove and 0 not upgraded. Need to get 24.8 MB of archives. After unpacking 104 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libsigsegv2 arm64 2.14-1+b2 [34.3 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 gawk arm64 1:5.2.1-2+b2 [644 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.22.5-4 [198 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.2-13 [91.4 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-5 [284 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.72-3 [493 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.22.5-4 [723 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.23 [90.6 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libtool all 2.5.4-2 [539 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 27 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.22.5-4 [1532 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.82.4-2 [1413 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 exonerate arm64 2.4.0-5+b2 [1730 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 mummer arm64 3.23+dfsg-8+b1 [643 kB] Fetched 24.8 MB in 0s (112 MB/s) Preconfiguring packages ... Selecting previously unselected package readline-common. (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 ... 19967 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../libsigsegv2_2.14-1+b2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.14-1+b2) ... Setting up readline-common (8.2-6) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up libsigsegv2:arm64 (2.14-1+b2) ... Selecting previously unselected package gawk. (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 ... 20009 files and directories currently installed.) Preparing to unpack .../00-gawk_1%3a5.2.1-2+b2_arm64.deb ... Unpacking gawk (1:5.2.1-2+b2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../01-liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.22.5-4_arm64.deb ... Unpacking gettext-base (0.22.5-4) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../07-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.2-13_arm64.deb ... Unpacking bsdextrautils (2.40.2-13) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../10-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-5_arm64.deb ... Unpacking m4 (1.4.19-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-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 .../16-autopoint_0.22.5-4_all.deb ... Unpacking autopoint (0.22.5-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.23_all.deb ... Unpacking libdebhelper-perl (13.23) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.5.4-2_all.deb ... Unpacking libtool (2.5.4-2) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-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 .../21-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../23-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../25-libunistring5_1.3-1_arm64.deb ... Unpacking libunistring5:arm64 (1.3-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../26-libicu72_72.1-6_arm64.deb ... Unpacking libicu72:arm64 (72.1-6) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../27-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/fsa-1.15.9+dfsg/ && 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 > ../fsa_1.15.9+dfsg-6_source.changes dpkg-buildpackage: info: source package fsa dpkg-buildpackage: info: source version 1.15.9+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean # found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:42: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.in:42: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.in:42: the top level configure.in:47: warning: The macro 'AC_HEADER_TIME' is obsolete. configure.in:47: You should run autoupdate. ./lib/autoconf/headers.m4:702: AC_HEADER_TIME is expanded from... configure.in:47: the top level configure.in:60: warning: The macro 'AC_LANG_CPLUSPLUS' is obsolete. configure.in:60: You should run autoupdate. ./lib/autoconf/c.m4:270: AC_LANG_CPLUSPLUS is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... acinclude.m4:5: AC_CXX_DYNAMIC_CAST is expanded from... configure.in:60: the top level configure.in:60: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:60: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:690: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... acinclude.m4:5: AC_CXX_DYNAMIC_CAST is expanded from... configure.in:60: the top level configure.in:268: warning: AC_OUTPUT should be used without arguments. configure.in:268: You should run autoupdate. configure.ac:3: warning: file 'version.m4' included several times dh_auto_configure ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '1111' is supported by ustar format... yes checking whether GID '1111' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for ar... ar checking the archiver (ar) interface... ar checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking for gawk... (cached) gawk checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for vfork.h... no checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for _Bool... no checking for stdbool.h that conforms to C99 or later... yes checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for unsigned long long int... yes checking for uintmax_t... yes checking for ptrdiff_t... yes checking for tr1/unordered_map... yes checking for tr1/unordered_set... yes checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking for floor... yes checking for memmove... yes checking for pow... yes checking for regcomp... yes checking for sqrt... yes checking for strchr... yes checking for strcspn... yes checking for strspn... yes checking for strstr... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking if gcc accepts -m64... no checking for mummer... /usr/bin/mummer checking for exonerate... /usr/bin/exonerate checking for g++ options needed to detect all undeclared functions... none needed checking for struct sysinfo.totalram... yes checking for struct sysinfo.mem_unit... yes checking whether sysctl is declared... no checking whether CTL_HW is declared... no checking whether HW_PHYSMEM is declared... no checking for javac... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/main/Makefile config.status: creating src/manager/Makefile config.status: creating src/fsa/Makefile config.status: creating src/annealing/Makefile config.status: creating src/math/Makefile config.status: creating src/util/Makefile config.status: creating src/seq/Makefile config.status: creating perl/Makefile config.status: creating examples/Makefile config.status: creating html/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands -- FSA 1.15.9 Configuration Results -- C++ compiler: g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG GCC version: gcc (Debian 14.2.0-12) 14.2.0 Host System type: aarch64-unknown-linux-gnu Install prefix: /usr See config.h for further configuration information. Email with questions and bug reports. dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' make all-recursive make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' Making all in src/util make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/util' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o dexception.o dexception.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o logfile.o logfile.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o memcheck.o memcheck.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o misc.o misc.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o opts_list.o opts_list.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o regexp.o regexp.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o sstring.o sstring.cc cc1plus: warning: '-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++ opts_list.cc:99:25: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 99 | SET_VERSION_INFO(*this); | ^ In file included from opts_list.cc:2: ../../src/util/opts_list.h:146:153: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 146 | #define SET_VERSION_INFO(OPTS) (OPTS).version_info.clear(); (OPTS).version_info << PACKAGE_STRING << " (" << DART_DEBUG_MODE_STRING << ") compiled " << __DATE__ << " " << __TIME__ << "\n"; | ^~~~~~~~ opts_list.cc:99:3: note: in expansion of macro 'SET_VERSION_INFO' 99 | SET_VERSION_INFO(*this); | ^~~~~~~~~~~~~~~~ regexp.cc: In member function 'char* CRegCompilerBase::regatom(int*)': regexp.cc:995:39: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 995 | register char ch; | ^~ In file included from misc.cc:8: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../../src/util/misc.h:14: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/util/logfile.h:13, from logfile.cc:1: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../src/util/logfile.h:8: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/util/sstring.h:14, from ../../src/util/dexception.h:6, from dexception.cc:4: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from ../../src/util/sstring.h:5: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/util/sstring.h:14, from sstring.cc:5: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from ../../src/util/sstring.h:5: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/util/sstring.h:14, from ../../src/util/dexception.h:6, from ../../src/util/opts_list.h:10: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../../src/util/opts_list.h:4: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ rm -f libutil.a ar cru libutil.a dexception.o logfile.o memcheck.o misc.o opts_list.o regexp.o sstring.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libutil.a make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/util' Making all in src/math make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/math' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o mathematics.o mathematics.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o mst.o mst.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ../../src/math/mst.h:11, from mst.cc:8: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../../src/util/misc.h:14: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/math/mathematics.h:23, from mathematics.cc:8: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from ../../src/math/mathematics.h:13: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ rm -f libmath.a ar cru libmath.a mathematics.o mst.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmath.a make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/math' Making all in src/seq make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/seq' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o alphabet.o alphabet.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o alignment.o alignment.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o gff.o gff.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o mercator.o mercator.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o sequence.o sequence.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o similarity_matrix.o similarity_matrix.cc cc1plus: warning: '-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++ In file included from ../../src/seq/sequence.h:19, from ../../src/seq/alignment.h:16, from ../../src/seq/mercator.h:13, from mercator.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/numeric:75, from mercator.cc:9: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/alphabet.h:20, from alphabet.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from ../../src/seq/alphabet.h:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, from ../../src/seq/alignment.h:16, from alignment.cc:13: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/numeric:75, from alignment.cc:8: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/math/mathematics.h:23, from sequence.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from ../../src/util/regexp.h:8, from sequence.cc:10: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/math/mathematics.h:23, from similarity_matrix.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from similarity_matrix.cc:8: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21, from sequence.cc:12: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/math/mathematics.h:23, from gff.cc:14: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from gff.cc:8: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from gff.cc:15: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21, from ../../src/seq/similarity_matrix.h:13, from similarity_matrix.cc:12: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ alignment.cc: In member function 'void fsa::Alignment::read_mfa(const std::string&, bool, bool)': alignment.cc:295:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = char; _Result = bool]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 295 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ alignment.cc:295:31: warning: 'constexpr std::unary_negate<_Predicate> std::not1(const _Predicate&) [with _Predicate = pointer_to_unary_function]' is deprecated: use 'std::not_fn' instead [-Wdeprecated-declarations] 295 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:1043:5: note: declared here 1043 | not1(const _Predicate& __pred) | ^~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ alignment.cc: In member function 'void fsa::Stockholm::read_stockholm(const std::string&, bool, bool)': alignment.cc:732:40: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = char; _Result = bool]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations] 732 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:1123:5: note: declared here 1123 | ptr_fun(_Result (*__x)(_Arg)) | ^~~~~~~ alignment.cc:732:26: warning: 'constexpr std::unary_negate<_Predicate> std::not1(const _Predicate&) [with _Predicate = pointer_to_unary_function]' is deprecated: use 'std::not_fn' instead [-Wdeprecated-declarations] 732 | std::not1 (std::ptr_fun (Alignment::is_gap_char))); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:1043:5: note: declared here 1043 | not1(const _Predicate& __pred) | ^~~~ rm -f libseq.a ar cru libseq.a alphabet.o alignment.o gff.o mercator.o sequence.o similarity_matrix.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseq.a make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/seq' Making all in src/manager make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/manager' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o manager.o manager.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o mw_adapter.o mw_adapter.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o db_adapter.o db_adapter.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o db_misc.o db_misc.cc cc1plus: warning: '-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++ In file included from ../../src/manager/manager.h:12, from manager.cc:6: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/anchors.h:17, from ../../src/fsa/fsa.h:71, from db_misc.cc:7: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from ../../src/fsa/anchors.h:20: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': ../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': ../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': ../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from ../../src/fsa/anchors.h:20, from ../../src/fsa/fsa.h:71, from manager.cc:8: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': ../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': ../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': ../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ rm -f libmanager.a ar cru libmanager.a manager.o mw_adapter.o db_adapter.o db_misc.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmanager.a make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/manager' Making all in src/fsa make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/fsa' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o algebras.o algebras.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o aminoacid_indel2dp.o aminoacid_indel2dp.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o aminoaciddp.o aminoaciddp.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o anchors.o anchors.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o constraints.o constraints.cc cc1plus: warning: '-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++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o fsa.o fsa.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o model.o model.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o nucleotide_indel2dp.o nucleotide_indel2dp.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o nucleotidedp.o nucleotidedp.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o sequence_pair_selector.o sequence_pair_selector.cc cc1plus: warning: '-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++ fsa.cc:25:125: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] ", "Distance-based alignment of DNA, RNA and proteins."); | ^ In file included from ../../src/fsa/fsa.h:66, from fsa.cc:11: ../../src/util/opts_list.h:146:153: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 146 | #define SET_VERSION_INFO(OPTS) (OPTS).version_info.clear(); (OPTS).version_info << PACKAGE_STRING << " (" << DART_DEBUG_MODE_STRING << ") compiled " << __DATE__ << " " << __TIME__ << "\n"; | ^~~~~~~~ ../../src/util/opts_list.h:152:153: note: in expansion of macro 'SET_VERSION_INFO' 152 | #define INIT_CONSTRUCTED_OPTS_LIST(OPTS,ARGS,SYNTAX,SHORTDESC) OPTS.short_description = (SHORTDESC); OPTS.syntax = (SYNTAX); OPTS.expect_args = (ARGS); SET_VERSION_INFO(OPTS); Log_stream::add_opts(OPTS); | ^~~~~~~~~~~~~~~~ fsa.cc:25:3: note: in expansion of macro 'INIT_CONSTRUCTED_OPTS_LIST' 25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] ", "Distance-based alignment of DNA, RNA and proteins."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from algebras.cc:27: algebras.h: In function 'BFloat double2bfloat(double)': algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from aminoacid_indel2dp.h:28, from aminoacid_indel2dp.cc:24: algebras.h: In function 'BFloat double2bfloat(double)': algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from nucleotide_indel2dp.h:28, from nucleotide_indel2dp.cc:24: algebras.h: In function 'BFloat double2bfloat(double)': algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from nucleotidedp.h:28, from nucleotidedp.cc:24: algebras.h: In function 'BFloat double2bfloat(double)': algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from aminoaciddp.h:28, from aminoaciddp.cc:24: algebras.h: In function 'BFloat double2bfloat(double)': algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ nucleotide_indel2dp.cc: In function 'Algebra Forward(NucleotideIndel2AlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': nucleotide_indel2dp.cc:789:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 789 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotide_indel2dp.cc:791:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 791 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotidedp.cc: In function 'Algebra Forward(NucleotideAlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': nucleotidedp.cc:789:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 789 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotidedp.cc:791:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 791 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotide_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotide_indel2dp.cc: In function 'Algebra BackwardBaumWelch(NucleotideIndel2AlignBaumWelch&, NucleotideIndel2AlignDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': nucleotide_indel2dp.cc:975:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 975 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotide_indel2dp.cc:977:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 977 | register bfloat iTempProb[3]; | ^~~~~~~~~ nucleotidedp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotidedp.cc: In function 'Algebra BackwardBaumWelch(NucleotideAlignBaumWelch&, NucleotideAlignDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': nucleotidedp.cc:945:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 945 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotidedp.cc:947:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 947 | register bfloat iTempProb[3]; | ^~~~~~~~~ nucleotide_indel2dp.cc: In function 'Algebra Backward(NucleotideIndel2AlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': nucleotide_indel2dp.cc:1277:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1277 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotide_indel2dp.cc:1279:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1279 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotidedp.cc: In function 'Algebra Backward(NucleotideAlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': nucleotidedp.cc:1187:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1187 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotidedp.cc:1189:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1189 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotidedp.cc:1166:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1166 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotide_indel2dp.cc:1256:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1256 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotidedp.cc: In function 'Algebra ForwardBanding(NucleotideAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotidedp.cc:1374:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1374 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotidedp.cc:1376:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1376 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotidedp.cc:1352:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1352 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotidedp.cc: In function 'Algebra BackwardBaumWelchBanding(NucleotideAlignWithBandingBaumWelch&, NucleotideAlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotidedp.cc:1567:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1567 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotidedp.cc:1569:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1569 | register bfloat iTempProb[3]; | ^~~~~~~~~ nucleotide_indel2dp.cc: In function 'Algebra ForwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotide_indel2dp.cc:1494:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1494 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotide_indel2dp.cc:1496:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1496 | register bfloat iTempProb[1]; | ^~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra Forward(AminoAcidIndel2AlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoacid_indel2dp.cc:821:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 821 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoacid_indel2dp.cc:823:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 823 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotide_indel2dp.cc:1472:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1472 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotidedp.cc: In function 'Algebra BackwardBanding(NucleotideAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotidedp.cc:1841:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1841 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotide_indel2dp.cc: In function 'Algebra BackwardBaumWelchBanding(NucleotideIndel2AlignWithBandingBaumWelch&, NucleotideIndel2AlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotide_indel2dp.cc:1717:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1717 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotidedp.cc:1843:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1843 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotide_indel2dp.cc:1719:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1719 | register bfloat iTempProb[3]; | ^~~~~~~~~ nucleotidedp.cc:1819:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1819 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoaciddp.cc: In function 'Algebra Forward(AminoAcidAlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoaciddp.cc:821:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 821 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoaciddp.cc:823:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 823 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotide_indel2dp.cc: In function 'Algebra BackwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotide_indel2dp.cc:2051:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2051 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotide_indel2dp.cc:2053:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2053 | register bfloat iTempProb[1]; | ^~~~~~~~~ aminoacid_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoaciddp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotide_indel2dp.cc:2029:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 2029 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra BackwardBaumWelch(AminoAcidIndel2AlignBaumWelch&, AminoAcidIndel2AlignDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoacid_indel2dp.cc:1039:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1039 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoacid_indel2dp.cc:1041:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1041 | register bfloat iTempProb[3]; | ^~~~~~~~~ aminoaciddp.cc: In function 'Algebra BackwardBaumWelch(AminoAcidAlignBaumWelch&, AminoAcidAlignDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoaciddp.cc:1009:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1009 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoaciddp.cc:1011:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1011 | register bfloat iTempProb[3]; | ^~~~~~~~~ aminoaciddp.cc: In function 'Algebra Backward(AminoAcidAlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoaciddp.cc:1283:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1283 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoaciddp.cc:1285:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1285 | register bfloat iTempProb[1]; | ^~~~~~~~~ aminoaciddp.cc:1230:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1230 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra Backward(AminoAcidIndel2AlignDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoacid_indel2dp.cc:1373:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1373 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoacid_indel2dp.cc:1375:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1375 | register bfloat iTempProb[1]; | ^~~~~~~~~ aminoaciddp.cc: In function 'Algebra ForwardBanding(AminoAcidAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoaciddp.cc:1502:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1502 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoaciddp.cc:1504:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1504 | register bfloat iTempProb[1]; | ^~~~~~~~~ aminoaciddp.cc:1448:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1448 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoaciddp.cc: In function 'Algebra BackwardBaumWelchBanding(AminoAcidAlignWithBandingBaumWelch&, AminoAcidAlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoaciddp.cc:1727:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1727 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoaciddp.cc:1729:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1729 | register bfloat iTempProb[3]; | ^~~~~~~~~ aminoacid_indel2dp.cc:1320:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1320 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoaciddp.cc: In function 'Algebra BackwardBanding(AminoAcidAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoaciddp.cc:2033:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2033 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoaciddp.cc:2035:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2035 | register bfloat iTempProb[1]; | ^~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra ForwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoacid_indel2dp.cc:1622:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1622 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoacid_indel2dp.cc:1624:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1624 | register bfloat iTempProb[1]; | ^~~~~~~~~ aminoaciddp.cc:1979:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1979 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc:1568:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1568 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra BackwardBaumWelchBanding(AminoAcidIndel2AlignWithBandingBaumWelch&, AminoAcidIndel2AlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoacid_indel2dp.cc:1877:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1877 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoacid_indel2dp.cc:1879:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1879 | register bfloat iTempProb[3]; | ^~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra BackwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoacid_indel2dp.cc:2243:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2243 | register double iTempResult[1]; | ^~~~~~~~~~~ aminoacid_indel2dp.cc:2245:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2245 | register bfloat iTempProb[1]; | ^~~~~~~~~ aminoacid_indel2dp.cc:2189:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 2189 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from model.cc:8: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': ../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': ../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': ../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from ../../src/fsa/anchors.h:17, from ../../src/fsa/fsa.h:71: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/anchors.h:17, from anchors.cc:16: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/model.h:32: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from ../../src/fsa/anchors.h:20: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': ../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': ../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': ../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from ../../src/fsa/anchors.h:20: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': ../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': ../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': ../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ anchors.cc: In member function 'fsa::Anchors fsa::Exonerate_adapter::call_exonerate(const std::string&, const std::string&, int) const': anchors.cc:863:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 863 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store exonerate results | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.cc:864:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 864 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.cc: In member function 'fsa::Anchors fsa::Mummer_adapter::call_mummer(const std::string&, const std::string&, size_t) const': anchors.cc:1100:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1100 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store mummer results | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.cc:1101:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1101 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f libfsa.a ar cru libfsa.a algebras.o aminoacid_indel2dp.o aminoaciddp.o anchors.o constraints.o fsa.o model.o nucleotide_indel2dp.o nucleotidedp.o sequence_pair_selector.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfsa.a make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/fsa' Making all in src/annealing make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/annealing' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o alignment_DAG.o alignment_DAG.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o dotplot.o dotplot.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o tree_weights.o tree_weights.cc cc1plus: warning: '-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++ In file included from dotplot.h:13, from dotplot.cc:8: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../../src/util/misc.h:14: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/util/logfile.h:13, from tree_weights.cc:8: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from ../../src/util/logfile.h:8: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, from ../../src/annealing/alignment_DAG.h:56, from alignment_DAG.cc:12: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, from /usr/include/c++/14/stack:62, from ../../src/annealing/alignment_DAG.h:39: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21, from ../../src/annealing/tree_weights.h:18, from tree_weights.cc:9: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from dotplot.h:14: ../../src/util/array2d.h:159:38: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 159 | struct xy_iterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21, from dotplot.h:15: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/annealing/alignment_DAG.h:58: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ ../../src/annealing/alignment_DAG.h: At global scope: ../../src/annealing/alignment_DAG.h:415:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 415 | class greater_index : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/annealing/alignment_DAG.h:426:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 426 | class smaller_index : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/annealing/alignment_DAG.h:436:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 436 | class smaller_weight : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/annealing/alignment_DAG.h:447:33: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 447 | class column_pair_hash : std::unary_function, bit64_t> { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ alignment_DAG.cc: In member function 'std::pair fsa::Column::get_accuracy_normalized(std::vector >&, const fsa::Tree_weights&, size_t) const': alignment_DAG.cc:28:174: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 28 | std::pair Column::get_accuracy_normalized (std::vector >& sparse_matrices, const Tree_weights& tree_weights, const size_t num_seqs) const { | ^~~~~ rm -f libannealing.a ar cru libannealing.a alignment_DAG.o dotplot.o tree_weights.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libannealing.a make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/annealing' Making all in src/main make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/main' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o main.o main.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o gapcleaner.o gapcleaner.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o isect_mercator_alignment_gff.o isect_mercator_alignment_gff.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o map_coords.o map_coords.cc cc1plus: warning: '-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++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o map_gff_coords.o map_gff_coords.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o percentid.o percentid.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o prot2codon.o prot2codon.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o slice_fasta.o slice_fasta.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o slice_fasta_gff.o slice_fasta_gff.cc cc1plus: warning: '-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++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o slice_mercator_alignment.o slice_mercator_alignment.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -c -o translate.o translate.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/include/c++/14/ext/hash_map:60, from ../../src/fsa/dptables.h:43, from ../../src/fsa/mybanding.h:25, from ../../src/fsa/model.h:24, from ../../src/fsa/anchors.h:20, from ../../src/fsa/fsa.h:71, from main.cc:8: /usr/include/c++/14/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from ../../src/fsa/fsa.h:65: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from ../../src/fsa/fsa.h:61: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/gff.h:17, from map_gff_coords.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from ../../src/seq/gff.h:12: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, from prot2codon.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from ../../src/seq/sequence.h:13: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:21, from ../../src/seq/alignment.h:16, from map_gff_coords.cc:12: ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21, from ../../src/fsa/fsa.h:68: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/gff.h:17, from isect_mercator_alignment_gff.cc:12: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from isect_mercator_alignment_gff.cc:9: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, from slice_fasta.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from ../../src/seq/sequence.h:13: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, from percentid.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from ../../src/seq/sequence.h:13: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/gff.h:17, from slice_fasta_gff.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from ../../src/seq/gff.h:12: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:21, from ../../src/seq/alignment.h:16, from isect_mercator_alignment_gff.cc:13: ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, from ../../src/seq/alignment.h:16, from slice_mercator_alignment.cc:12: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from slice_mercator_alignment.cc:9: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/annealing/dotplot.h:14, from ../../src/fsa/anchors.h:16: ../../src/util/array2d.h:159:38: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 159 | struct xy_iterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:19, from translate.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from ../../src/seq/sequence.h:13: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/fsa/anchors.h:17: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/seq/sequence.h:19, from ../../src/seq/alignment.h:16, from map_coords.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/sequence.h:21, from slice_fasta_gff.cc:12: ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/set:62, from ../../src/seq/alignment.h:13: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/fsa/anchors.h:18: ../../src/annealing/alignment_DAG.h: At global scope: ../../src/annealing/alignment_DAG.h:415:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 415 | class greater_index : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/annealing/alignment_DAG.h:426:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 426 | class smaller_index : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/annealing/alignment_DAG.h:436:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 436 | class smaller_weight : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/annealing/alignment_DAG.h:447:33: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 447 | class column_pair_hash : std::unary_function, bit64_t> { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': ../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': ../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': ../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from ../../src/seq/sequence.h:19, from ../../src/annealing/alignment_DAG.h:56, from gapcleaner.cc:11: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/deque:67, from /usr/include/c++/14/stack:62, from ../../src/annealing/alignment_DAG.h:39: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/util/misc.h:203:34: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 203 | struct Map_value_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from ../../src/seq/interval.h:13, from ../../src/seq/sequence.h:21: ../../src/seq/gff.h:185:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 185 | struct GFF_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/seq/interval.h:112:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 112 | struct Genomic_interval_less : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -Wl,-z,relro -Wl,-z,now -o prot2codon prot2codon.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -Wl,-z,relro -Wl,-z,now -o map_gff_coords map_gff_coords.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_fasta slice_fasta.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -Wl,-z,relro -Wl,-z,now -o translate translate.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_mercator_alignment slice_mercator_alignment.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a In file included from ../../src/annealing/alignment_DAG.h:58: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ ../../src/annealing/alignment_DAG.h: At global scope: ../../src/annealing/alignment_DAG.h:415:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 415 | class greater_index : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/annealing/alignment_DAG.h:426:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 426 | class smaller_index : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/annealing/alignment_DAG.h:436:31: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 436 | class smaller_weight : std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../../src/annealing/alignment_DAG.h:447:33: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 447 | class column_pair_hash : std::unary_function, bit64_t> { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -Wl,-z,relro -Wl,-z,now -o percentid percentid.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -Wl,-z,relro -Wl,-z,now -o isect_mercator_alignment_gff isect_mercator_alignment_gff.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_fasta_gff slice_fasta_gff.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -Wl,-z,relro -Wl,-z,now -o map_coords map_coords.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -Wl,-z,relro -Wl,-z,now -o fsa main.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DNDEBUG -Wl,-z,relro -Wl,-z,now -o gapcleaner gapcleaner.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/main' Making all in perl make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/perl' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/perl' Making all in examples make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/examples' Making all in html make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/html' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/html' Making all in tests make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/tests' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' make[1]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' echo "Tests seem to miss some files:" Tests seem to miss some files: echo "make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop." make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop. make[1]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/fsa/ make -j12 install DESTDIR=/build/reproducible-path/fsa-1.15.9\+dfsg/debian/fsa AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' Making install in src/util make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/util' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/util' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/util' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/util' Making install in src/math make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/math' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/math' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/math' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/math' Making install in src/seq make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/seq' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/seq' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/seq' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/seq' Making install in src/manager make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/manager' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/manager' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/manager' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/manager' Making install in src/fsa make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/fsa' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/fsa' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/fsa' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/fsa' Making install in src/annealing make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/annealing' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/annealing' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/annealing' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/annealing' Making install in src/main make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/main' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/main' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/fsa-1.15.9+dfsg/debian/fsa/usr/bin' /usr/bin/install -c fsa gapcleaner isect_mercator_alignment_gff map_coords map_gff_coords percentid prot2codon slice_fasta slice_fasta_gff slice_mercator_alignment translate '/build/reproducible-path/fsa-1.15.9+dfsg/debian/fsa/usr/bin' make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/main' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/main' Making install in perl make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/perl' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/perl' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/perl' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/perl' Making install in examples make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/examples' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/examples' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/examples' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/examples' Making install in html make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/html' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/html' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/html' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/html' Making install in tests make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/tests' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/tests' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/tests' make[2]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' make[1]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' dh_install mv /build/reproducible-path/fsa-1.15.9+dfsg/debian/fsa/usr/bin/translate /build/reproducible-path/fsa-1.15.9+dfsg/debian/fsa/usr/bin/fsa-translate make[1]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'fsa' in '../fsa_1.15.9+dfsg-6_arm64.deb'. dpkg-deb: building package 'fsa-dbgsym' in '../fsa-dbgsym_1.15.9+dfsg-6_arm64.deb'. # found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate dpkg-genbuildinfo --build=binary -O../fsa_1.15.9+dfsg-6_arm64.buildinfo dpkg-genchanges --build=binary -O../fsa_1.15.9+dfsg-6_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2038800 and its subdirectories I: Current time: Fri Jan 17 20:47:44 -12 2025 I: pbuilder-time-stamp: 1737190064 Sat Jan 18 08:47:46 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Sat Jan 18 08:47:46 UTC 2025 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Sat Jan 18 08:50:53 UTC 2025 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Sat Jan 18 08:50:53 UTC 2025 I: fsa_1.15.9+dfsg-6_arm64.changes: Format: 1.8 Date: Sun, 15 Nov 2020 17:45:20 +0100 Source: fsa Binary: fsa fsa-dbgsym Architecture: arm64 Version: 1.15.9+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: fsa - Fast Statistical Alignment of protein, RNA or DNA sequences Changes: fsa (1.15.9+dfsg-6) unstable; urgency=medium . * Fix typo Checksums-Sha1: bf49757b020e340458a8c3f4a70e5520634d9bfa 16016304 fsa-dbgsym_1.15.9+dfsg-6_arm64.deb a73932f10e904475ff73f7a025c11925c100aa87 5272 fsa_1.15.9+dfsg-6_arm64.buildinfo 6c0bfd51d56615b1739da95095cecec4b7f49fc4 633768 fsa_1.15.9+dfsg-6_arm64.deb Checksums-Sha256: 749224700afff01737cd058037bb09bf364278a5b5206a416470edb06586b17a 16016304 fsa-dbgsym_1.15.9+dfsg-6_arm64.deb 6546f3b5f0fdabdc84dc79e41192a3a6d13882f1604a3ee405d67a463a9f2203 5272 fsa_1.15.9+dfsg-6_arm64.buildinfo 73e2ffc9690788d85d25d3b90ae7b068c6b1b02400d067714a6c6b860ecdf476 633768 fsa_1.15.9+dfsg-6_arm64.deb Files: 94bc5f076e229e995e1534e4af13c84f 16016304 debug optional fsa-dbgsym_1.15.9+dfsg-6_arm64.deb 6fc71b137f369b983406413b132844eb 5272 science optional fsa_1.15.9+dfsg-6_arm64.buildinfo 5f81ba6f6d7ea2cd7327d9519b1fb5c9 633768 science optional fsa_1.15.9+dfsg-6_arm64.deb Sat Jan 18 08:50:54 UTC 2025 I: diffoscope 285 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_16-45306.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.lfnEWkho/fsa_1.15.9+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.lfnEWkho/fsa_1.15.9+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.lfnEWkho/fsa_1.15.9+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.lfnEWkho/b1/fsa_1.15.9+dfsg-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.lfnEWkho/b2/fsa_1.15.9+dfsg-6_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.490s) 0.490s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.160s) 0.160s 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: 814ms CPU time consumed: 813ms Sat Jan 18 08:50:56 UTC 2025 I: diffoscope 285 found no differences in the changes files, and a .buildinfo file also exists. Sat Jan 18 08:50:56 UTC 2025 I: fsa from trixie built successfully and reproducibly on arm64. Sat Jan 18 08:50:57 UTC 2025 I: Submitting .buildinfo files to external archives: Sat Jan 18 08:50:57 UTC 2025 I: Submitting 8.0K b1/fsa_1.15.9+dfsg-6_arm64.buildinfo.asc Sat Jan 18 08:50:58 UTC 2025 I: Submitting 8.0K b2/fsa_1.15.9+dfsg-6_arm64.buildinfo.asc Sat Jan 18 08:50:59 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Jan 18 08:50:59 UTC 2025 I: Done submitting .buildinfo files. Sat Jan 18 08:50:59 UTC 2025 I: Removing signed fsa_1.15.9+dfsg-6_arm64.buildinfo.asc files: removed './b1/fsa_1.15.9+dfsg-6_arm64.buildinfo.asc' removed './b2/fsa_1.15.9+dfsg-6_arm64.buildinfo.asc'