I: pbuilder: network access will be disabled during build I: Current time: Tue May 14 15:32:13 +14 2024 I: pbuilder-time-stamp: 1715650333 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [fsa_1.15.9+dfsg-6.dsc] I: copying [./fsa_1.15.9+dfsg.orig.tar.xz] I: copying [./fsa_1.15.9+dfsg-6.debian.tar.xz] I: Extracting source 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/2656503/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 14 01:32 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2656503/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2656503/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=c4c0d1e2d85a47cda1cd65ed90c3bed1 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2656503 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.1iHyvrFn/pbuilderrc_Z6w7 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1iHyvrFn/b2 --logfile b2/build.log fsa_1.15.9+dfsg-6.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 11 11:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2656503/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19699 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on exonerate; however: Package exonerate is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} exonerate{a} file{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libglib2.0-0t64{a} libicu72{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libreadline8t64{a} libsigsegv2{a} 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 24.3 MB of archives. After unpacking 95.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libsigsegv2 amd64 2.14-1+b1 [34.3 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 gawk amd64 1:5.2.1-2+b1 [674 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7 [15.0 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 28 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 exonerate amd64 2.4.0-5+b1 [1963 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Fetched 24.3 MB in 1s (21.1 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 ... 19699 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.14-1+b1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.14-1+b1) ... Setting up readline-common (8.2-4) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libsigsegv2:amd64 (2.14-1+b1) ... 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 ... 19741 files and directories currently installed.) Preparing to unpack .../00-gawk_1%3a5.2.1-2+b1_amd64.deb ... Unpacking gawk (1:5.2.1-2+b1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../01-liblocale-gettext-perl_1.07-7_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... 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%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../07-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../10-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_amd64.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 libelf1t64:amd64. Preparing to unpack .../24-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../26-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../27-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-14+b1_amd64.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 libglib2.0-0t64:amd64. Preparing to unpack .../32-libglib2.0-0t64_2.80.2-1_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.80.2-1) ... Selecting previously unselected package exonerate. Preparing to unpack .../33-exonerate_2.4.0-5+b1_amd64.deb ... Unpacking exonerate (2.4.0-5+b1) ... Selecting previously unselected package help2man. Preparing to unpack .../34-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package mummer. Preparing to unpack .../35-mummer_3.23+dfsg-8_amd64.deb ... Unpacking mummer (3.23+dfsg-8) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up gawk (1:5.2.1-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.80.2-1) ... No schema files found: doing nothing. Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up mummer (3.23+dfsg-8) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up exonerate (2.4.0-5+b1) ... Setting up liblocale-gettext-perl (1.07-7) ... 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 groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2656503/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2656503/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/fsa-1.15.9+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 amd64 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=x86_64-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/x86_64-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 '2222' is supported by ustar format... yes checking whether GID '2222' 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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking if gcc accepts -m64... yes 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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG GCC version: gcc (Debian 13.2.0-24) 13.2.0 Host System type: x86_64-pc-linux-gnu Install prefix: /usr See config.h for further configuration information. Email with questions and bug reports. dh_auto_build make -j20 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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o logfile.o logfile.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o memcheck.o memcheck.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o opts_list.o opts_list.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o regexp.o regexp.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o sstring.o sstring.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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); | ^~~~~~~~~~~~~~~~ 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 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 | ^~~~~~~~~~~~~~~ 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 ../../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 | ^~~~~~~~~~~~~~~ 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 | ^~~~~~~~~~~~~~~ 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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o mst.o mst.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ../../src/math/mst.h:11, from mst.cc:8: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o mercator.o mercator.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o sequence.o sequence.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o similarity_matrix.o similarity_matrix.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ 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/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 | ^~~~~~~~~~~~~~~ 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 | ^~~~~~~~~~~~~~~ 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/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 | ^~~~~~~~~~~~~~~ ../../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 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 | ^~~~~~~~~~~~~~~ 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 ../../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 { | ^~~~~~~~~~~~~~~ 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 | ^~~~~~~~~~~~~~~ /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/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 | ^~~~~~~~~~~~~~~ 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))); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ ../../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: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) | ^~~~ /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) | ^~~~ 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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o db_misc.o db_misc.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from ../../src/fsa/anchors.h:17, from ../../src/fsa/fsa.h:71, from db_misc.cc:7: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from ../../src/fsa/anchors.h:20: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': ../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': ../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': ../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from ../../src/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/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from ../../src/fsa/anchors.h:20, from ../../src/fsa/fsa.h:71, from manager.cc:8: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': ../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': ../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': ../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ rm -f libmanager.a ar cru libmanager.a manager.o mw_adapter.o db_adapter.o db_misc.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmanager.a make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/manager' Making all in src/fsa make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/fsa' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o anchors.o anchors.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o constraints.o constraints.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o fsa.o fsa.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o nucleotidedp.o nucleotidedp.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o sequence_pair_selector.o sequence_pair_selector.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ fsa.cc:25:125: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] ", "Distance-based alignment of DNA, RNA and proteins."); | ^ In file included from ../../src/fsa/fsa.h:66, from fsa.cc:11: ../../src/util/opts_list.h:146:153: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 146 | #define SET_VERSION_INFO(OPTS) (OPTS).version_info.clear(); (OPTS).version_info << PACKAGE_STRING << " (" << DART_DEBUG_MODE_STRING << ") compiled " << __DATE__ << " " << __TIME__ << "\n"; | ^~~~~~~~ ../../src/util/opts_list.h:152:153: note: in expansion of macro 'SET_VERSION_INFO' 152 | #define INIT_CONSTRUCTED_OPTS_LIST(OPTS,ARGS,SYNTAX,SHORTDESC) OPTS.short_description = (SHORTDESC); OPTS.syntax = (SYNTAX); OPTS.expect_args = (ARGS); SET_VERSION_INFO(OPTS); Log_stream::add_opts(OPTS); | ^~~~~~~~~~~~~~~~ fsa.cc:25:3: note: in expansion of macro 'INIT_CONSTRUCTED_OPTS_LIST' 25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] ", "Distance-based alignment of DNA, RNA and proteins."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from algebras.cc:27: algebras.h: In function 'BFloat double2bfloat(double)': algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from aminoacid_indel2dp.h:28, from aminoacid_indel2dp.cc:24: algebras.h: In function 'BFloat double2bfloat(double)': algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from nucleotide_indel2dp.h:28, from nucleotide_indel2dp.cc:24: algebras.h: In function 'BFloat double2bfloat(double)': algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from 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); | ^~ 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]; | ^~~~~~~~~ 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); | ^~ 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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ aminoacid_indel2dp.cc:2189:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 2189 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoaciddp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotide_indel2dp.cc:1256:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1256 | 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 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: 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: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 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]; | ^~~~~~~~~~~ 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]; | ^~~~~~~~~~~ nucleotidedp.cc:791:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 791 | register bfloat iTempProb[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]; | ^~~~~~~~~ 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]; | ^~~~~~~~~ nucleotidedp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotidedp.cc: In function 'Algebra BackwardBaumWelch(NucleotideAlignBaumWelch&, NucleotideAlignDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&)': nucleotidedp.cc:945:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 945 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotidedp.cc:947:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 947 | register bfloat iTempProb[3]; | ^~~~~~~~~ nucleotide_indel2dp.cc:2029:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 2029 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoaciddp.cc: In function 'Algebra BackwardBanding(AminoAcidAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoaciddp.cc:2033:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2033 | register double iTempResult[1]; | ^~~~~~~~~~~ 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]; | ^~~~~~~~~~~ aminoaciddp.cc:2035:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 2035 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotidedp.cc:1189:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1189 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotidedp.cc:1166:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1166 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoaciddp.cc:1979:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1979 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotidedp.cc: In function 'Algebra ForwardBanding(NucleotideAlignWithBandingDPTable**, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotidedp.cc:1374:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1374 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotidedp.cc:1376:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1376 | register bfloat iTempProb[1]; | ^~~~~~~~~ nucleotidedp.cc:1352:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1352 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotidedp.cc: In function 'Algebra BackwardBaumWelchBanding(NucleotideAlignWithBandingBaumWelch&, NucleotideAlignWithBandingDPTable*, const std::string&, const std::string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotidedp.cc:1567:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1567 | register double iTempResult[1]; | ^~~~~~~~~~~ nucleotidedp.cc:1569:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 1569 | register bfloat iTempProb[3]; | ^~~~~~~~~ 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; | ^~~~~~~~~~~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from model.cc:8: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': ../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': ../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': ../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from ../../src/fsa/anchors.h:17, from ../../src/fsa/fsa.h:71: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/anchors.h:17, from anchors.cc:16: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/model.h:32: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from ../../src/fsa/anchors.h:20: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': ../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': ../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': ../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ In file included from ../../src/fsa/nucleotidedp.h:28, from ../../src/fsa/model.h:25, from ../../src/fsa/anchors.h:20: ../../src/fsa/algebras.h: In function 'BFloat double2bfloat(double)': ../../src/fsa/algebras.h:195:21: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 195 | register BFloat a( 0.0, 0 ); | ^ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:211:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 211 | register BFloat sf(a.f*b.f,a.e+b.e); | ^~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)': ../../src/fsa/algebras.h:218:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 218 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)': ../../src/fsa/algebras.h:231:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 231 | register double mantisse = a.f*b; | ^~~~~~~~ ../../src/fsa/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)': ../../src/fsa/algebras.h:238:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 238 | register BFloat sf(a.f/b.f, a.e-b.e); | ^~ anchors.cc: In member function 'fsa::Anchors fsa::Exonerate_adapter::call_exonerate(const std::string&, const std::string&, int) const': anchors.cc:863:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 863 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store exonerate results | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.cc:864:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 864 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.cc: In member function 'fsa::Anchors fsa::Mummer_adapter::call_mummer(const std::string&, const std::string&, size_t) const': anchors.cc:1100:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1100 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store mummer results | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.cc:1101:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1101 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f libfsa.a ar cru libfsa.a algebras.o aminoacid_indel2dp.o aminoaciddp.o anchors.o constraints.o fsa.o model.o nucleotide_indel2dp.o nucleotidedp.o sequence_pair_selector.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfsa.a make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/fsa' Making all in src/annealing make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/annealing' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o tree_weights.o tree_weights.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from dotplot.h:13, from dotplot.cc:8: ../../src/util/misc.h:187:30: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 187 | struct Duple_less : std::binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o isect_mercator_alignment_gff.o isect_mercator_alignment_gff.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o map_coords.o map_coords.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o prot2codon.o prot2codon.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o slice_fasta.o slice_fasta.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o slice_fasta_gff.o slice_fasta_gff.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -c -o translate.o translate.cc cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ In file included from /usr/include/c++/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/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 | ^~~~~~~~~~~~~~~ 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/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/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: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 | ^~~~~~~~~~~~~~~ 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/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 | ^~~~~~~~~~~~~~~ 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/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 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 | ^~~~~~~~~~~~~~~ ../../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 | ^~~~~~~~~~~~~~~ ../../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 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 | ^~~~~~~~~~~~~~~ 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/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/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 | ^~~~~~~~~~~~~~~ ../../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: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 | ^~~~~~~~~~~~~~~ ../../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/fsa/anchors.h:17: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const fsa::Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/seq/sequence.h:19, from 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/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 | ^~~~~~~~~~~~~~~ ../../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/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 { | ^~~~~~~~~~~~~~~ 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 | ^~~~~~~~~~~~~~~ /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 { | ^~~~~~~~~~~~~~~ ../../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 | ^~~~~~~~~~~~~~~ /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/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 | ^~~~~~~~~~~~~~~ ../../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/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/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/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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/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 | ^~~~~ g++ -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ../../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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -Wl,-z,relro -Wl,-z,now -o map_gff_coords map_gff_coords.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -Wl,-z,relro -Wl,-z,now -o fsa main.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -m64 -O3 -ffast-math -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/fsa-1.15.9+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DNDEBUG -Wl,-z,relro -Wl,-z,now -o gapcleaner gapcleaner.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/src/main' Making all in perl make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/perl' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/perl' Making all in examples make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/examples' Making all in html make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/html' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/html' Making all in tests make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg/tests' make[3]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' make[3]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' make[2]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' make[1]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/fsa-1.15.9+dfsg' echo "Tests seem to miss some files:" Tests seem to miss some files: echo "make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop." make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop. make[1]: Leaving directory '/build/reproducible-path/fsa-1.15.9+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/fsa/ make -j20 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-dbgsym' in '../fsa-dbgsym_1.15.9+dfsg-6_amd64.deb'. dpkg-deb: building package 'fsa' in '../fsa_1.15.9+dfsg-6_amd64.deb'. # found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate dpkg-genbuildinfo --build=binary -O../fsa_1.15.9+dfsg-6_amd64.buildinfo dpkg-genchanges --build=binary -O../fsa_1.15.9+dfsg-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2656503/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2656503/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2656503 and its subdirectories I: Current time: Tue May 14 15:50:02 +14 2024 I: pbuilder-time-stamp: 1715651402