Wed Apr 3 14:48:58 UTC 2024 I: starting to build fsa/trixie/i386 on jenkins on '2024-04-03 14:48' Wed Apr 3 14:48:58 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_6/18128/console.log Wed Apr 3 14:48:58 UTC 2024 I: Downloading source for trixie/fsa=1.15.9+dfsg-6 --2024-04-03 14:48:58-- http://deb.debian.org/debian/pool/main/f/fsa/fsa_1.15.9%2bdfsg-6.dsc Connecting to 78.137.99.97:3128... 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% 280M=0s 2024-04-03 14:48:58 (280 MB/s) - ‘fsa_1.15.9+dfsg-6.dsc’ saved [1971/1971] Wed Apr 3 14:48:58 UTC 2024 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----- Wed Apr 3 14:48:58 UTC 2024 I: Checking whether the package is not for us Wed Apr 3 14:48:58 UTC 2024 I: Starting 1st build on remote node ionos6-i386.debian.net. Wed Apr 3 14:48:59 UTC 2024 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Wed Apr 3 14:50:36 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 6 09:12:01 -12 2025 I: pbuilder-time-stamp: 1746565921 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: using eatmydata during job 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 gpgv: Signature made Sun Nov 15 17:07:02 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./fsa_1.15.9+dfsg-6.dsc: no acceptable signature found 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/29660/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='94b7cc31ec6447ac884add3d7dd093be' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='29660' 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.ni6buZfe/pbuilderrc_LruP --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.ni6buZfe/b1 --logfile b1/build.log fsa_1.15.9+dfsg-6.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos6-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 5 17:48 /bin -> usr/bin I: user script /srv/workspace/pbuilder/29660/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19876 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} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{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, 39 newly installed, 0 to remove and 0 not upgraded. Need to get 24.4 MB of archives. After unpacking 95.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-3 [69.1 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libreadline8 i386 8.2-3+b1 [171 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libsigsegv2 i386 2.14-1 [37.5 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 gawk i386 1:5.2.1-2 [680 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-6+b1 [15.3 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 28 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libglib2.0-0 i386 2.78.4-1 [1520 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 exonerate i386 2.4.0-5 [1749 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 mummer i386 3.23+dfsg-8 [669 kB] Fetched 24.4 MB in 0s (91.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19876 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../libreadline8_8.2-3+b1_i386.deb ... Unpacking libreadline8:i386 (8.2-3+b1) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../libsigsegv2_2.14-1_i386.deb ... Unpacking libsigsegv2:i386 (2.14-1) ... Setting up readline-common (8.2-3) ... Setting up libreadline8:i386 (8.2-3+b1) ... Setting up libsigsegv2:i386 (2.14-1) ... 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 ... 19910 files and directories currently installed.) Preparing to unpack .../00-gawk_1%3a5.2.1-2_i386.deb ... Unpacking gawk (1:5.2.1-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../01-liblocale-gettext-perl_1.07-6+b1_i386.deb ... Unpacking liblocale-gettext-perl (1.07-6+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../04-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-3_i386.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../10-libpipeline1_1.5.7-1+b2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1+b2) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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 libsub-override-perl. Preparing to unpack .../21-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../24-libelf1_0.190-1+b1_i386.deb ... Unpacking libelf1:i386 (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../26-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../27-libxml2_2.9.14+dfsg-1.3+b2_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../32-libglib2.0-0_2.78.4-1_i386.deb ... Unpacking libglib2.0-0:i386 (2.78.4-1) ... Selecting previously unselected package exonerate. Preparing to unpack .../33-exonerate_2.4.0-5_i386.deb ... Unpacking exonerate (2.4.0-5) ... Selecting previously unselected package help2man. Preparing to unpack .../34-help2man_1.49.3_i386.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package mummer. Preparing to unpack .../35-mummer_3.23+dfsg-8_i386.deb ... Unpacking mummer (3.23+dfsg-8) ... Setting up libpipeline1:i386 (1.5.7-1+b2) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up gawk (1:5.2.1-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:i386 (2.78.4-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1:i386 (1:5.45-2+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up mummer (3.23+dfsg-8) ... Setting up libsub-override-perl (0.10-1) ... Setting up libelf1:i386 (0.190-1+b1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Setting up exonerate (2.4.0-5) ... Setting up liblocale-gettext-perl (1.07-6+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... 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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 i386 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 cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead 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.m4:704: 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.m4:743: 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.m4:262: AC_LANG_CPLUSPLUS is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: 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.m4:2847: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: 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. dh_auto_configure ./configure --build=i686-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/i386-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... 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... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu 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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG GCC version: gcc (Debian 13.2.0-13) 13.2.0 Host System type: i686-pc-linux-gnu Install prefix: /usr See config.h for further configuration information. Email with questions and bug reports. dh_auto_build make -j22 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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sstring.o sstring.cc 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../../src/util/misc.h:14: /usr/include/c++/13/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++/13/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++/13/string:49, from ../../src/util/sstring.h:5: /usr/include/c++/13/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++/13/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../src/util/logfile.h:8: /usr/include/c++/13/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++/13/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++/13/string:49, from ../../src/util/sstring.h:5: /usr/include/c++/13/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++/13/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../../src/util/opts_list.h:4: /usr/include/c++/13/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++/13/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mst.o mst.cc 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../../src/util/misc.h:14: /usr/include/c++/13/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++/13/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++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ../../src/math/mathematics.h:13: /usr/include/c++/13/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++/13/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o similarity_matrix.o similarity_matrix.cc 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++/13/string:49, from ../../src/seq/alphabet.h:15: /usr/include/c++/13/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++/13/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 ../../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++/13/numeric:75, from mercator.cc:9: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/numeric:75, from alignment.cc:8: /usr/include/c++/13/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++/13/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++/13/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++/13/string:49, from ../../src/util/regexp.h:8, from sequence.cc:10: /usr/include/c++/13/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++/13/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++/13/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from gff.cc:8: /usr/include/c++/13/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++/13/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++/13/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++/13/bits/stl_function.h:1126:5: note: declared here 1126 | 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++/13/bits/stl_function.h:1046:5: note: declared here 1046 | not1(const _Predicate& __pred) | ^~~~ 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++/13/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++/13/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++/13/bits/stl_function.h:1126:5: note: declared here 1126 | 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++/13/bits/stl_function.h:1046:5: note: declared here 1046 | not1(const _Predicate& __pred) | ^~~~ 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from similarity_matrix.cc:8: /usr/include/c++/13/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++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o db_misc.o db_misc.cc 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, 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); | ^~ 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); | ^~ 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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o constraints.o constraints.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o model.o model.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o nucleotide_indel2dp.o nucleotide_indel2dp.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o nucleotidedp.o nucleotidedp.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sequence_pair_selector.o sequence_pair_selector.cc 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 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); | ^~ 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); | ^~ 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]; | ^~~~~~~~~ aminoaciddp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ 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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ 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; | ^~~~~~~~~~~~~~ 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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ 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: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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ nucleotidedp.cc:1352:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1352 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ 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]; | ^~~~~~~~~ aminoaciddp.cc:1979:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1979 | 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:1472:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1472 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ 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]; | ^~~~~~~~~~~ nucleotide_indel2dp.cc:1719:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1719 | register bfloat iTempProb[3]; | ^~~~~~~~~ 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]; | ^~~~~~~~~~~ nucleotidedp.cc:1843:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1843 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotidedp.cc:1819:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1819 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ 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]; | ^~~~~~~~~ nucleotide_indel2dp.cc:2029:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 2029 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ 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); | ^~ 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]; | ^~~~~~~~~ aminoacid_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | 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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ aminoacid_indel2dp.cc:1320:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1320 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ 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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ 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); | ^~ 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/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/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/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/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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o tree_weights.o tree_weights.cc 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../../src/util/misc.h:14: /usr/include/c++/13/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++/13/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from ../../src/util/logfile.h:8: /usr/include/c++/13/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++/13/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++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from /usr/include/c++/13/stack:62, from ../../src/annealing/alignment_DAG.h:39: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ 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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o map_coords.o map_coords.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o map_gff_coords.o map_gff_coords.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o percentid.o percentid.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o prot2codon.o prot2codon.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta_gff.o slice_fasta_gff.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_mercator_alignment.o slice_mercator_alignment.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o translate.o translate.cc In file included from /usr/include/c++/13/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++/13/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/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++/13/string:49, from ../../src/seq/gff.h:12: /usr/include/c++/13/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++/13/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++/13/string:49, from ../../src/seq/gff.h:12: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/string:49, from ../../src/seq/sequence.h:13: /usr/include/c++/13/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++/13/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++/13/string:49, from ../../src/seq/sequence.h:13: /usr/include/c++/13/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++/13/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from isect_mercator_alignment_gff.cc:9: /usr/include/c++/13/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++/13/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++/13/string:49, from ../../src/seq/sequence.h:13: /usr/include/c++/13/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++/13/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++/13/string:49, from ../../src/seq/sequence.h:13: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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 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 /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from ../../src/seq/alignment.h:13: /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct 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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../../src/fsa/fsa.h:61: /usr/include/c++/13/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++/13/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++/13/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++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from slice_mercator_alignment.cc:9: /usr/include/c++/13/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++/13/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++/13/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 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++/13/bits/refwrap.h:39, from /usr/include/c++/13/deque:67, from /usr/include/c++/13/stack:62, from ../../src/annealing/alignment_DAG.h:39: /usr/include/c++/13/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++/13/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++/13/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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 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++/13/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/13/string:47: /usr/include/c++/13/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ 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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_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 | ^~~~~ g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 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++/13/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++/13/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++/13/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++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 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); | ^~ g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 g++ -Wall -Wno-tautological-compare -march=i686 -O3 -ffast-math -g -O2 -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 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 -j22 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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'fsa' in '../fsa_1.15.9+dfsg-6_i386.deb'. dpkg-deb: building package 'fsa-dbgsym' in '../fsa-dbgsym_1.15.9+dfsg-6_i386.deb'. # found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate dpkg-genbuildinfo --build=binary -O../fsa_1.15.9+dfsg-6_i386.buildinfo dpkg-genchanges --build=binary -O../fsa_1.15.9+dfsg-6_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/29660 and its subdirectories I: Current time: Tue May 6 09:13:35 -12 2025 I: pbuilder-time-stamp: 1746566015 Wed Apr 3 14:50:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Wed Apr 3 14:50:36 UTC 2024 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Wed Apr 3 14:53:27 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. Wed Apr 3 14:53:27 UTC 2024 I: fsa_1.15.9+dfsg-6_i386.changes: Format: 1.8 Date: Sun, 15 Nov 2020 17:45:20 +0100 Source: fsa Binary: fsa fsa-dbgsym Architecture: i386 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: 612cce26c7905da782b82fdc5dd7b2680ac99095 15970112 fsa-dbgsym_1.15.9+dfsg-6_i386.deb 86aa46e6cfe2d55fef0b8aa643ce928b7b12a737 5656 fsa_1.15.9+dfsg-6_i386.buildinfo 8ced53f41891765982bcc00633ae078812a7cddc 727372 fsa_1.15.9+dfsg-6_i386.deb Checksums-Sha256: ac0fcab7fd9a3e8978b562762c27d0a33e08253d373ad89d55884f11d8971216 15970112 fsa-dbgsym_1.15.9+dfsg-6_i386.deb 328f0ec802f5494ea6a6942ef0a8d6289ec2441937595653bc00d0fe273ed429 5656 fsa_1.15.9+dfsg-6_i386.buildinfo ce8f4ad287ec1a961d138ba3ad9223bdc95e3007c425b61231198cae4cf48739 727372 fsa_1.15.9+dfsg-6_i386.deb Files: 53ac31786f7519ec18440c27ade1108b 15970112 debug optional fsa-dbgsym_1.15.9+dfsg-6_i386.deb f0808cbb9170afcd46b4cc55b360061f 5656 science optional fsa_1.15.9+dfsg-6_i386.buildinfo 7460cf6f8b6452e10acd2636e04dc625 727372 science optional fsa_1.15.9+dfsg-6_i386.deb Wed Apr 3 14:53:29 UTC 2024 I: diffoscope 262 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_6-18128.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ni6buZfe/fsa_1.15.9+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ni6buZfe/fsa_1.15.9+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ni6buZfe/fsa_1.15.9+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ni6buZfe/b1/fsa_1.15.9+dfsg-6_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.ni6buZfe/b2/fsa_1.15.9+dfsg-6_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.495s) 0.495s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.188s) 0.188s 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: 811ms CPU time consumed: 812ms Wed Apr 3 14:53:30 UTC 2024 I: diffoscope 262 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 3 14:53:30 UTC 2024 I: fsa from trixie built successfully and reproducibly on i386. Wed Apr 3 14:53:31 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Apr 3 14:53:31 UTC 2024 I: Submitting 8.0K b1/fsa_1.15.9+dfsg-6_i386.buildinfo.asc Wed Apr 3 14:53:32 UTC 2024 I: Submitting 8.0K b2/fsa_1.15.9+dfsg-6_i386.buildinfo.asc Wed Apr 3 14:53:33 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 3 14:53:33 UTC 2024 I: Done submitting .buildinfo files. Wed Apr 3 14:53:33 UTC 2024 I: Removing signed fsa_1.15.9+dfsg-6_i386.buildinfo.asc files: removed './b1/fsa_1.15.9+dfsg-6_i386.buildinfo.asc' removed './b2/fsa_1.15.9+dfsg-6_i386.buildinfo.asc'