Diff of the two buildlogs: -- --- b1/build.log 2024-04-28 23:57:31.738960602 +0000 +++ b2/build.log 2024-04-28 23:18:54.573829526 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 28 11:18:57 -12 2024 -I: pbuilder-time-stamp: 1714346337 +I: Current time: Sun Jun 1 18:48:28 +14 2025 +I: pbuilder-time-stamp: 1748753308 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/308189/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2391872/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 1 04:48 /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/2391872/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2391872/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="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=42 ' + 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='6617abaa9c06481481c8f46cf4623727' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='308189' - PS1='# ' - PS2='> ' + INVOCATION_ID=567d49b2e628402f9362a62c059f9e6a + 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=2391872 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.M0mydieY/pbuilderrc_Z3um --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.M0mydieY/b1 --logfile b1/build.log exonerate_2.4.0-5.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.M0mydieY/pbuilderrc_RiZP --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.M0mydieY/b2 --logfile b2/build.log exonerate_2.4.0-5.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 22 13:10 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/308189/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 27 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2391872/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -90,7 +122,7 @@ Depends: debhelper-compat (= 13), libglib2.0-dev, libreadline-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19900 files and directories currently installed.) +(Reading database ... 19724 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: @@ -238,32 +270,31 @@ Get: 66 http://deb.debian.org/debian trixie/main amd64 libncurses6 amd64 6.4+20240414-1 [104 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libncurses-dev amd64 6.4+20240414-1 [349 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libreadline-dev amd64 8.2-4 [152 kB] -Fetched 36.1 MB in 1s (26.1 MB/s) +Fetched 36.1 MB in 16s (2215 kB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. -(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 ... 19900 files and directories currently installed.) +(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 ... 19724 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64:amd64. -(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 ... 19893 files and directories currently installed.) +(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 ... 19717 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: - libkrb5-3:amd64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). -(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 ... 19899 files and directories currently installed.) +(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 ... 19723 files and directories currently installed.) Removing libssl3:amd64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:amd64. -(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 ... 19886 files and directories currently installed.) +(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 ... 19710 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_amd64.deb ... Unpacking libssl3t64:amd64 (3.2.1-3) ... Setting up libssl3t64:amd64 (3.2.1-3) ... Selecting previously unselected package libpython3.11-minimal:amd64. -(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 ... 19901 files and directories currently installed.) +(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 ... 19725 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. @@ -276,7 +307,7 @@ Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. -(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 ... 20217 files and directories currently installed.) +(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 ... 20041 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. @@ -309,7 +340,7 @@ Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. -(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 ... 21209 files and directories currently installed.) +(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 ... 21033 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sensible-utils. @@ -488,8 +519,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Apr 28 23:20:47 UTC 2024. -Universal Time is now: Sun Apr 28 23:20:47 UTC 2024. +Local time is now: Sun Jun 1 04:50:17 UTC 2025. +Universal Time is now: Sun Jun 1 04:50:17 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -552,7 +583,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/exonerate-2.4.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../exonerate_2.4.0-5_source.changes +I: user script /srv/workspace/pbuilder/2391872/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2391872/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/exonerate-2.4.0/ && 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 > ../exonerate_2.4.0-5_source.changes dpkg-buildpackage: info: source package exonerate dpkg-buildpackage: info: source version 2.4.0-5 dpkg-buildpackage: info: source distribution unstable @@ -712,7 +747,7 @@ config.status: creating test/data/protein/Makefile config.status: executing depfiles commands dh_auto_build - make -j20 + make -j42 make[1]: Entering directory '/build/reproducible-path/exonerate-2.4.0' Making all in doc make[2]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc' @@ -755,6 +790,9 @@ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bitarray.test.o bitarray.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bitarray.o bitarray.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splaytree.test.o splaytree.test.c +gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splaytree.o splaytree.c +gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o noitree.test.o noitree.test.c +gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o noitree.o noitree.c rangetree.c: In function 'RangeTree_insert_recent': rangetree.c:151:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] 151 | g_tree_traverse(rt->recent_data, RangeTree_insert_recent_collect, @@ -765,10 +803,7 @@ /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ -gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splaytree.o splaytree.c -gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o noitree.test.o noitree.test.c -gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o noitree.o noitree.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sparsecache.test sparsecache.test.o sparsecache.o -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o recyclebin.test recyclebin.test.o recyclebin.o -lglib-2.0 bitarray.c: In function 'BitArray_read': bitarray.c:83:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 83 | fread(ba->data, sizeof(guchar), size, fp); @@ -777,17 +812,17 @@ bitarray.c:189:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 189 | fread(&num, sizeof(guint64), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o dejavu.test dejavu.test.o dejavu.o -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o recyclebin.test recyclebin.test.o recyclebin.o -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o slist.test slist.test.o slist.o recyclebin.o -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sparsecache.test sparsecache.test.o sparsecache.o -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o splaytree.test splaytree.test.o splaytree.o recyclebin.o -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o noitree.test noitree.test.o noitree.o recyclebin.o splaytree.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o vfsm.test vfsm.test.o vfsm.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o rangetree.test rangetree.test.o rangetree.o recyclebin.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o matrix.test matrix.test.o matrix.o -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o bitarray.test bitarray.test.o bitarray.o -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o slist.test slist.test.o slist.o recyclebin.o -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o rangetree.test rangetree.test.o rangetree.o recyclebin.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fsm.test fsm.test.o fsm.o recyclebin.o -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o bitarray.test bitarray.test.o bitarray.o -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o dejavu.test dejavu.test.o dejavu.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o pqueue.test pqueue.test.o pqueue.o recyclebin.o -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o splaytree.test splaytree.test.o splaytree.o recyclebin.o -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o noitree.test noitree.test.o noitree.o recyclebin.o splaytree.o -lglib-2.0 make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/struct' Making all in general make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/general' @@ -803,19 +838,6 @@ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o jobqueue.o jobqueue.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o threadref.test.o threadref.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o threadref.o threadref.c -jobqueue.test.c: In function 'main': -jobqueue.test.c:34:13: warning: Deprecated pre-processor symbol - 34 | if(!g_thread_supported()) - | ^~~~~~~~~~~~~~~~~ -jobqueue.test.c:35:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] - 35 | g_thread_init(NULL); - | ^~~~~~~~~~~~~ -In file included from /usr/include/glib-2.0/glib.h:115, - from jobqueue.h:23, - from jobqueue.test.c:17: -/usr/include/glib-2.0/glib/deprecated/gthread.h:267:10: note: declared here - 267 | void g_thread_init (gpointer vtable); - | ^~~~~~~~~~~~~ argument.c: In function 'ArgumentParse_boolean': argument.c:138:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 138 | if(!g_strcasecmp(arg_string, true_string[i])) @@ -863,6 +885,20 @@ /usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here 148 | void g_tree_traverse (GTree *tree, | ^~~~~~~~~~~~~~~ +jobqueue.test.c: In function 'main': +jobqueue.test.c:34:13: warning: Deprecated pre-processor symbol + 34 | if(!g_thread_supported()) + | ^~~~~~~~~~~~~~~~~ +jobqueue.test.c:35:9: warning: 'g_thread_init' is deprecated [-Wdeprecated-declarations] + 35 | g_thread_init(NULL); + | ^~~~~~~~~~~~~ +In file included from /usr/include/glib-2.0/glib.h:115, + from jobqueue.h:23, + from jobqueue.test.c:17: +/usr/include/glib-2.0/glib/deprecated/gthread.h:267:10: note: declared here + 267 | void g_thread_init (gpointer vtable); + | ^~~~~~~~~~~~~ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o threadref.test threadref.test.o threadref.o -lpthread -lglib-2.0 socket.c: In function 'Socket_send': socket.c:168:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 168 | g_string_sprintfa(full_msg, "linecount: %d\n", line_count+1); @@ -893,7 +929,6 @@ | ^~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o jobqueue.test jobqueue.test.o jobqueue.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o lineparse.test lineparse.test.o lineparse.o -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o threadref.test threadref.test.o threadref.o -lpthread -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o socket.test socket.test.o socket.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o compoundfile.test compoundfile.test.o compoundfile.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o argument.test argument.test.o argument.o -lglib-2.0 @@ -912,6 +947,16 @@ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o alphabet.test.o alphabet.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codonsubmat.test.o codonsubmat.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codonsubmat.o codonsubmat.c +sequence.c: In function 'Sequence_destroy_annotation_tree': +sequence.c:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] + 97 | g_tree_traverse(tree, Sequence_destroy_annotation_data, + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/glib-2.0/glib.h:95, + from sequence.h:24, + from sequence.c:21: +/usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here + 148 | void g_tree_traverse (GTree *tree, + | ^~~~~~~~~~~~~~~ alphabet.c: In function 'Alphabet_name_get_type': alphabet.c:317:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 317 | if(!g_strcasecmp(name, dna_string[i])) @@ -936,16 +981,6 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ -sequence.c: In function 'Sequence_destroy_annotation_tree': -sequence.c:97:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] - 97 | g_tree_traverse(tree, Sequence_destroy_annotation_data, - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/glib-2.0/glib.h:95, - from sequence.h:24, - from sequence.c:21: -/usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here - 148 | void g_tree_traverse (GTree *tree, - | ^~~~~~~~~~~~~~~ splice.c: In function 'SplicePredictor_parse_data': splice.c:146:17: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 146 | if(!g_strcasecmp(word, "splice")) @@ -972,11 +1007,11 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o alphabet.test alphabet.test.o alphabet.o ../../src/general/argument.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o submat.test submat.test.o submat.o -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o alphabet.test alphabet.test.o alphabet.o ../../src/general/argument.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o translate.test translate.test.o translate.o ../../src/general/argument.o -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o splice.test splice.test.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sequence.test sequence.test.o sequence.o alphabet.o translate.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o splice.test splice.test.o splice.o ../../src/struct/matrix.o ../../src/struct/sparsecache.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o codonsubmat.test codonsubmat.test.o codonsubmat.o ../../src/general/argument.o -lm -lglib-2.0 make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/sequence' Making all in comparison @@ -1332,7 +1367,6 @@ alignment.c:987:5: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 987 | g_strup(qy_codon); | ^~~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o region.test region.test.o region.o -lglib-2.0 /usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here 277 | gchar* g_strup (gchar *string); | ^~~~~~~ @@ -1363,9 +1397,10 @@ viterbi.c:965:5: note: in expansion of macro 'g_string_free' 965 | g_string_free(str, FALSE); | ^~~~~~~~~~~~~ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o region.test region.test.o region.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o codegen.test codegen.test.o codegen.o ../../src/general/argument.o -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o layout.test layout.test.o layout.o ../../src/struct/matrix.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o subopt.test subopt.test.o subopt.o region.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o layout.test layout.test.o layout.o ../../src/struct/matrix.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o c4.test c4.test.o c4.o region.o ../../src/struct/matrix.o ../../src/general/threadref.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o cgutil.test cgutil.test.o cgutil.o codegen.o c4.o region.o ../../src/general/argument.o ../../src/struct/matrix.o ../../src/general/threadref.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o alignment.test alignment.test.o alignment.o c4.o region.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/general/threadref.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o -lm -lglib-2.0 @@ -1400,8 +1435,8 @@ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o boundary.test.o boundary.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o scheduler.test.o scheduler.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/struct -I../../src/comparison -I../../src/sequence -I../../src/general -I../../src/c4 -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o straceback.test.o straceback.test.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o lookahead.test lookahead.test.o lookahead.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o straceback.test straceback.test.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o lookahead.test lookahead.test.o lookahead.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o boundary.test boundary.test.o boundary.o ../../src/general/argument.o ../../src/c4/region.o -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o sdp.test sdp.test.o sdp.o boundary.o scheduler.o lookahead.o straceback.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o scheduler.test scheduler.test.o scheduler.o lookahead.o boundary.o straceback.o ../../src/struct/recyclebin.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/c4/c4.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/codegen.o ../../src/c4/region.o ../../src/c4/layout.o ../../src/c4/viterbi.o ../../src/c4/subopt.o ../../src/c4/cgutil.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 @@ -1439,13 +1474,7 @@ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o modeltype.test.o modeltype.test.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o modeltype.o modeltype.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bootstrapper.o bootstrapper.c -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o frameshift.test frameshift.test.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o edit_distance.test edit_distance.test.o edit_distance.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o affine.test affine.test.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o protein2dna.test protein2dna.test.o protein2dna.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o ner.test ner.test.o ner.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o ungapped.test ungapped.test.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o coding2coding.test coding2coding.test.o coding2coding.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 421 | if((!models) || (!g_strcasecmp(models, "all"))) @@ -1459,6 +1488,7 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o edit_distance.test edit_distance.test.o edit_distance.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 modeltype.c: In function 'Model_Type_from_string': modeltype.c:121:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 121 | if(!g_strcasecmp(name[i], str)) @@ -1478,6 +1508,11 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o frameshift.test frameshift.test.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o affine.test affine.test.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o protein2dna.test protein2dna.test.o protein2dna.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o ner.test ner.test.o ner.o affine.o ungapped.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o coding2coding.test coding2coding.test.o coding2coding.o affine.o ungapped.o frameshift.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o est2genome.test est2genome.test.o est2genome.o affine.o ungapped.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o intron.test intron.test.o intron.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o protein2genome.test protein2genome.test.o protein2genome.o protein2dna.o ungapped.o intron.o affine.o frameshift.o phase.o ../../src/struct/slist.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/alignment.o ../../src/c4/region.o ../../src/c4/c4.o ../../src/c4/subopt.o ../../src/comparison/match.o ../../src/sequence/codonsubmat.o ../../src/sequence/submat.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 @@ -1590,1432 +1625,1432 @@ Making all in program make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/program' ../../src/model/bootstrapper --compiled no -** Message: 11:22:05.921: Starting building bootstrapping components -** Message: 11:22:05.921: Processing model [u] -** Message: 11:22:05.922: Bootstrapper processing model [ungapped:dna2dna] -** Message: 11:22:05.923: Process optimal [optimal:ungapped:dna2dna] +** Message: 18:51:45.707: Starting building bootstrapping components +** Message: 18:51:45.707: Processing model [u] +** Message: 18:51:45.708: Bootstrapper processing model [ungapped:dna2dna] +** Message: 18:51:45.709: Process optimal [optimal:ungapped:dna2dna] -** (process:412491): WARNING **: 11:22:05.923: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen] +** (process:2479568): WARNING **: 18:51:45.709: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen] -** (process:412491): WARNING **: 11:22:05.923: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen] +** (process:2479568): WARNING **: 18:51:45.710: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen] -** (process:412491): WARNING **: 11:22:05.923: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu] +** (process:2479568): WARNING **: 18:51:45.710: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu] -** (process:412491): WARNING **: 11:22:05.924: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu] -** Message: 11:22:05.931: Compiling codegen: +** (process:2479568): WARNING **: 18:51:45.710: Creating codegen directory [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu] +** Message: 18:51:45.710: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.c -** Message: 11:22:06.906: Compiling codegen: +** Message: 18:51:47.113: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.c -** Message: 11:22:07.487: Compiling codegen: +** Message: 18:51:47.819: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.c -** Message: 11:22:08.343: Compiling codegen: +** Message: 18:51:48.314: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c -** Message: 11:22:09.124: Compiling codegen: +** Message: 18:51:49.134: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 11:22:09.933: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] -** Message: 11:22:09.933: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive +** Message: 18:51:51.851: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] +** Message: 18:51:51.851: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive ar -cSq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -** Message: 11:22:09.950: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] -** Message: 11:22:09.950: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] -** Message: 11:22:09.950: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive +** Message: 18:51:51.943: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] +** Message: 18:51:51.944: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] +** Message: 18:51:51.944: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -** Message: 11:22:09.961: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] -** Message: 11:22:09.961: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] -** Message: 11:22:09.961: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive +** Message: 18:51:52.013: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] +** Message: 18:51:52.014: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] +** Message: 18:51:52.014: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -** Message: 11:22:09.969: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] -** Message: 11:22:09.969: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] -** Message: 11:22:09.969: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 18:51:52.097: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] +** Message: 18:51:52.098: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] +** Message: 18:51:52.098: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -** Message: 11:22:09.980: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] -** Message: 11:22:09.980: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 11:22:09.981: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive +** Message: 18:51:52.163: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] +** Message: 18:51:52.163: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 18:51:52.163: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 11:22:09.991: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] -** Message: 11:22:09.991: Bootstrapper processing model [ungapped:protein2protein] -** Message: 11:22:09.992: Process optimal [optimal:ungapped:protein2protein] -** Message: 11:22:09.992: Compiling codegen: +** Message: 18:51:52.228: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] +** Message: 18:51:52.229: Bootstrapper processing model [ungapped:protein2protein] +** Message: 18:51:52.229: Process optimal [optimal:ungapped:protein2protein] +** Message: 18:51:52.229: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.c -** Message: 11:22:10.400: Compiling codegen: +** Message: 18:51:52.571: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.c -** Message: 11:22:10.929: Compiling codegen: +** Message: 18:51:53.017: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.c -** Message: 11:22:11.471: Compiling codegen: +** Message: 18:51:54.027: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c -** Message: 11:22:12.139: Compiling codegen: +** Message: 18:51:54.798: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c -** Message: 11:22:13.313: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] -** Message: 11:22:13.314: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive +** Message: 18:51:56.433: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] +** Message: 18:51:56.433: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -** Message: 11:22:13.347: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] -** Message: 11:22:13.347: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] -** Message: 11:22:13.347: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive +** Message: 18:51:56.473: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] +** Message: 18:51:56.474: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] +** Message: 18:51:56.474: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -** Message: 11:22:13.386: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] -** Message: 11:22:13.386: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] -** Message: 11:22:13.386: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive +** Message: 18:51:56.663: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] +** Message: 18:51:56.664: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] +** Message: 18:51:56.665: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -** Message: 11:22:13.426: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] -** Message: 11:22:13.426: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] -** Message: 11:22:13.426: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive +** Message: 18:51:56.730: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] +** Message: 18:51:56.730: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] +** Message: 18:51:56.730: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -** Message: 11:22:13.478: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] -** Message: 11:22:13.479: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] -** Message: 11:22:13.479: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive +** Message: 18:51:57.014: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] +** Message: 18:51:57.014: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] +** Message: 18:51:57.014: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -** Message: 11:22:13.490: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] -** Message: 11:22:13.491: Bootstrapper processing model [ungapped:dna2protein] -** Message: 11:22:13.491: Process optimal [optimal:ungapped:dna2protein] -** Message: 11:22:13.492: Compiling codegen: +** Message: 18:51:57.246: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] +** Message: 18:51:57.246: Bootstrapper processing model [ungapped:dna2protein] +** Message: 18:51:57.246: Process optimal [optimal:ungapped:dna2protein] +** Message: 18:51:57.247: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.c -** Message: 11:22:14.651: Compiling codegen: +** Message: 18:51:57.906: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.c -** Message: 11:22:15.799: Compiling codegen: +** Message: 18:51:59.422: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.c -** Message: 11:22:16.743: Compiling codegen: +** Message: 18:52:00.417: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c -** Message: 11:22:17.959: Compiling codegen: +** Message: 18:52:01.751: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c -** Message: 11:22:19.382: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] -** Message: 11:22:19.383: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive +** Message: 18:52:03.596: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] +** Message: 18:52:03.597: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -** Message: 11:22:19.418: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] -** Message: 11:22:19.419: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] -** Message: 11:22:19.419: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive +** Message: 18:52:03.618: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] +** Message: 18:52:03.619: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] +** Message: 18:52:03.619: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -** Message: 11:22:19.444: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] -** Message: 11:22:19.444: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] -** Message: 11:22:19.444: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive +** Message: 18:52:03.631: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] +** Message: 18:52:03.631: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] +** Message: 18:52:03.631: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -** Message: 11:22:19.462: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] -** Message: 11:22:19.462: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] -** Message: 11:22:19.462: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive +** Message: 18:52:03.644: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] +** Message: 18:52:03.645: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] +** Message: 18:52:03.645: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -** Message: 11:22:19.474: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] -** Message: 11:22:19.474: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] -** Message: 11:22:19.474: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive +** Message: 18:52:03.659: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] +** Message: 18:52:03.660: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] +** Message: 18:52:03.660: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -** Message: 11:22:19.490: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] -** Message: 11:22:19.490: Bootstrapper processing model [ungapped:protein2dna] -** Message: 11:22:19.490: Process optimal [optimal:ungapped:protein2dna] -** Message: 11:22:19.491: Compiling codegen: +** Message: 18:52:03.688: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] +** Message: 18:52:03.688: Bootstrapper processing model [ungapped:protein2dna] +** Message: 18:52:03.689: Process optimal [optimal:ungapped:protein2dna] +** Message: 18:52:03.689: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.c -** Message: 11:22:20.148: Compiling codegen: +** Message: 18:52:04.958: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.c -** Message: 11:22:20.939: Compiling codegen: +** Message: 18:52:06.044: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.c -** Message: 11:22:21.791: Compiling codegen: +** Message: 18:52:07.057: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c -** Message: 11:22:22.999: Compiling codegen: +** Message: 18:52:08.856: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c -** Message: 11:22:24.134: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] -** Message: 11:22:24.134: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive +** Message: 18:52:09.908: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] +** Message: 18:52:09.908: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -** Message: 11:22:24.198: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] -** Message: 11:22:24.199: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] -** Message: 11:22:24.199: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive +** Message: 18:52:09.919: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] +** Message: 18:52:09.920: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] +** Message: 18:52:09.920: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -** Message: 11:22:24.246: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] -** Message: 11:22:24.247: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] -** Message: 11:22:24.247: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive +** Message: 18:52:09.957: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] +** Message: 18:52:09.957: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] +** Message: 18:52:09.957: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -** Message: 11:22:24.282: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] -** Message: 11:22:24.282: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] -** Message: 11:22:24.282: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive +** Message: 18:52:09.976: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] +** Message: 18:52:09.977: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] +** Message: 18:52:09.977: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -** Message: 11:22:24.330: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] -** Message: 11:22:24.330: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] -** Message: 11:22:24.330: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive +** Message: 18:52:09.992: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] +** Message: 18:52:09.993: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] +** Message: 18:52:09.993: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -** Message: 11:22:24.354: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] -** Message: 11:22:24.355: Processing model [u:t] -** Message: 11:22:24.355: Bootstrapper processing model [ungapped:codon] -** Message: 11:22:24.356: Process optimal [optimal:ungapped:codon] -** Message: 11:22:24.363: Compiling codegen: +** Message: 18:52:10.012: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] +** Message: 18:52:10.013: Processing model [u:t] +** Message: 18:52:10.013: Bootstrapper processing model [ungapped:codon] +** Message: 18:52:10.013: Process optimal [optimal:ungapped:codon] +** Message: 18:52:10.014: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.c -** Message: 11:22:25.355: Compiling codegen: +** Message: 18:52:10.590: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.c -** Message: 11:22:26.444: Compiling codegen: +** Message: 18:52:11.250: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.c -** Message: 11:22:27.988: Compiling codegen: +** Message: 18:52:12.711: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c -** Message: 11:22:29.877: Compiling codegen: +** Message: 18:52:16.763: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c -** Message: 11:22:31.586: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] -** Message: 11:22:31.586: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive +** Message: 18:52:20.338: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] +** Message: 18:52:20.338: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o -** Message: 11:22:31.606: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] -** Message: 11:22:31.607: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] -** Message: 11:22:31.608: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive +** Message: 18:52:20.582: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] +** Message: 18:52:20.583: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] +** Message: 18:52:20.583: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o -** Message: 11:22:31.639: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] -** Message: 11:22:31.640: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] -** Message: 11:22:31.640: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive +** Message: 18:52:20.770: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] +** Message: 18:52:20.770: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] +** Message: 18:52:20.771: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o -** Message: 11:22:31.682: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] -** Message: 11:22:31.686: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] -** Message: 11:22:31.687: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive +** Message: 18:52:20.922: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] +** Message: 18:52:20.922: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] +** Message: 18:52:20.922: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -** Message: 11:22:31.718: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] -** Message: 11:22:31.719: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] -** Message: 11:22:31.719: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive +** Message: 18:52:21.097: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] +** Message: 18:52:21.097: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] +** Message: 18:52:21.097: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -** Message: 11:22:31.762: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] -** Message: 11:22:31.762: Processing model [a:g] -** Message: 11:22:31.763: Bootstrapper processing model [affine:global:dna2dna] -** Message: 11:22:31.763: Process optimal [optimal:affine:global:dna2dna] -** Message: 11:22:31.764: Compiling codegen: +** Message: 18:52:21.460: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] +** Message: 18:52:21.460: Processing model [a:g] +** Message: 18:52:21.460: Bootstrapper processing model [affine:global:dna2dna] +** Message: 18:52:21.460: Process optimal [optimal:affine:global:dna2dna] +** Message: 18:52:21.562: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c -** Message: 11:22:33.208: Compiling codegen: +** Message: 18:52:23.606: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c -** Message: 11:22:35.520: Compiling codegen: +** Message: 18:52:25.158: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c -** Message: 11:22:37.144: Compiling codegen: +** Message: 18:52:28.690: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 11:22:39.263: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] -** Message: 11:22:39.263: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive +** Message: 18:52:31.157: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] +** Message: 18:52:31.158: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -** Message: 11:22:39.286: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] -** Message: 11:22:39.287: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] -** Message: 11:22:39.287: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive +** Message: 18:52:31.541: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] +** Message: 18:52:31.541: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] +** Message: 18:52:31.541: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -** Message: 11:22:39.330: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] -** Message: 11:22:39.331: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] -** Message: 11:22:39.331: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 18:52:31.861: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] +** Message: 18:52:31.861: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] +** Message: 18:52:31.861: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -** Message: 11:22:39.362: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] -** Message: 11:22:39.362: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 11:22:39.362: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive +** Message: 18:52:32.313: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] +** Message: 18:52:32.313: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 18:52:32.313: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 11:22:39.391: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] -** Message: 11:22:39.391: Bootstrapper processing model [affine:global:protein2protein] -** Message: 11:22:39.392: Process optimal [optimal:affine:global:protein2protein] -** Message: 11:22:39.393: Compiling codegen: +** Message: 18:52:32.477: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] +** Message: 18:52:32.477: Bootstrapper processing model [affine:global:protein2protein] +** Message: 18:52:32.477: Process optimal [optimal:affine:global:protein2protein] +** Message: 18:52:32.478: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c -** Message: 11:22:40.641: Compiling codegen: +** Message: 18:52:34.518: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c -** Message: 11:22:42.937: Compiling codegen: +** Message: 18:52:38.647: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c -** Message: 11:22:44.571: Compiling codegen: +** Message: 18:52:40.378: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c -** Message: 11:22:46.744: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] -** Message: 11:22:46.744: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive +** Message: 18:52:43.574: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] +** Message: 18:52:43.575: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -** Message: 11:22:46.774: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] -** Message: 11:22:46.775: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] -** Message: 11:22:46.775: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive +** Message: 18:52:43.612: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] +** Message: 18:52:43.612: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] +** Message: 18:52:43.612: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -** Message: 11:22:46.815: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] -** Message: 11:22:46.815: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] -** Message: 11:22:46.815: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive +** Message: 18:52:43.654: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] +** Message: 18:52:43.654: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] +** Message: 18:52:43.654: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -** Message: 11:22:46.883: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] -** Message: 11:22:46.883: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] -** Message: 11:22:46.883: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive +** Message: 18:52:43.682: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] +** Message: 18:52:43.682: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] +** Message: 18:52:43.683: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -** Message: 11:22:46.934: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] -** Message: 11:22:46.935: Processing model [a:b] -** Message: 11:22:46.935: Bootstrapper processing model [affine:bestfit:dna2dna] -** Message: 11:22:46.935: Process optimal [optimal:affine:bestfit:dna2dna] -** Message: 11:22:46.937: Compiling codegen: +** Message: 18:52:43.708: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] +** Message: 18:52:43.708: Processing model [a:b] +** Message: 18:52:43.708: Bootstrapper processing model [affine:bestfit:dna2dna] +** Message: 18:52:43.708: Process optimal [optimal:affine:bestfit:dna2dna] +** Message: 18:52:43.709: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c -** Message: 11:22:48.672: Compiling codegen: +** Message: 18:52:47.694: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c -** Message: 11:22:52.016: Compiling codegen: +** Message: 18:52:50.317: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c -** Message: 11:22:54.831: Compiling codegen: +** Message: 18:52:52.785: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c -** Message: 11:22:56.828: Compiling codegen: +** Message: 18:52:54.961: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 11:22:59.134: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] -** Message: 11:22:59.134: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive +** Message: 18:52:56.639: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] +** Message: 18:52:56.639: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -** Message: 11:22:59.342: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] -** Message: 11:22:59.342: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] -** Message: 11:22:59.342: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive +** Message: 18:52:57.109: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] +** Message: 18:52:57.110: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] +** Message: 18:52:57.110: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -** Message: 11:22:59.494: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] -** Message: 11:22:59.494: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] -** Message: 11:22:59.495: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive +** Message: 18:52:57.355: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] +** Message: 18:52:57.355: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] +** Message: 18:52:57.355: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -** Message: 11:22:59.550: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] -** Message: 11:22:59.551: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] -** Message: 11:22:59.551: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 18:52:57.737: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] +** Message: 18:52:57.737: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] +** Message: 18:52:57.737: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -** Message: 11:22:59.623: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] -** Message: 11:22:59.623: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 11:22:59.623: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive +** Message: 18:52:57.854: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] +** Message: 18:52:57.854: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 18:52:57.855: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 11:22:59.676: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] -** Message: 11:22:59.676: Bootstrapper processing model [affine:bestfit:protein2protein] -** Message: 11:22:59.676: Process optimal [optimal:affine:bestfit:protein2protein] -** Message: 11:22:59.677: Compiling codegen: +** Message: 18:52:58.061: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] +** Message: 18:52:58.062: Bootstrapper processing model [affine:bestfit:protein2protein] +** Message: 18:52:58.062: Process optimal [optimal:affine:bestfit:protein2protein] +** Message: 18:52:58.063: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c -** Message: 11:23:01.312: Compiling codegen: +** Message: 18:53:00.660: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c -** Message: 11:23:03.585: Compiling codegen: +** Message: 18:53:04.572: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c -** Message: 11:23:05.516: Compiling codegen: +** Message: 18:53:08.266: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c -** Message: 11:23:07.357: Compiling codegen: +** Message: 18:53:11.195: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c -** Message: 11:23:09.095: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] -** Message: 11:23:09.095: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive +** Message: 18:53:12.737: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] +** Message: 18:53:12.738: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -** Message: 11:23:09.311: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] -** Message: 11:23:09.312: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] -** Message: 11:23:09.312: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive +** Message: 18:53:12.769: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] +** Message: 18:53:12.769: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] +** Message: 18:53:12.769: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -** Message: 11:23:09.520: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] -** Message: 11:23:09.521: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] -** Message: 11:23:09.521: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive +** Message: 18:53:12.798: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] +** Message: 18:53:12.798: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] +** Message: 18:53:12.798: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -** Message: 11:23:09.641: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] -** Message: 11:23:09.643: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] -** Message: 11:23:09.644: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive +** Message: 18:53:12.873: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] +** Message: 18:53:12.873: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] +** Message: 18:53:12.873: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -** Message: 11:23:10.048: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] -** Message: 11:23:10.049: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] -** Message: 11:23:10.049: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive +** Message: 18:53:12.906: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] +** Message: 18:53:12.907: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] +** Message: 18:53:12.907: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -** Message: 11:23:10.394: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] -** Message: 11:23:10.394: Processing model [a:l] -** Message: 11:23:10.394: Bootstrapper processing model [affine:local:dna2dna] -** Message: 11:23:10.394: Process optimal [optimal:affine:local:dna2dna] -** Message: 11:23:10.395: Compiling codegen: +** Message: 18:53:12.959: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] +** Message: 18:53:12.959: Processing model [a:l] +** Message: 18:53:12.960: Bootstrapper processing model [affine:local:dna2dna] +** Message: 18:53:12.960: Process optimal [optimal:affine:local:dna2dna] +** Message: 18:53:12.960: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c -** Message: 11:23:11.135: Compiling codegen: +** Message: 18:53:14.149: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c -** Message: 11:23:12.219: Compiling codegen: +** Message: 18:53:15.276: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c -** Message: 11:23:13.112: Compiling codegen: +** Message: 18:53:16.919: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c -** Message: 11:23:14.632: Compiling codegen: +** Message: 18:53:20.730: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 11:23:16.307: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] -** Message: 11:23:16.307: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive +** Message: 18:53:22.175: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] +** Message: 18:53:22.175: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -** Message: 11:23:16.622: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] -** Message: 11:23:16.623: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] -** Message: 11:23:16.623: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive +** Message: 18:53:22.211: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] +** Message: 18:53:22.211: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] +** Message: 18:53:22.211: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -** Message: 11:23:16.939: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] -** Message: 11:23:16.940: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] -** Message: 11:23:16.940: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive +** Message: 18:53:22.252: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] +** Message: 18:53:22.253: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] +** Message: 18:53:22.253: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -** Message: 11:23:17.005: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] -** Message: 11:23:17.006: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] -** Message: 11:23:17.006: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 18:53:22.286: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] +** Message: 18:53:22.286: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] +** Message: 18:53:22.286: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -** Message: 11:23:17.140: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] -** Message: 11:23:17.140: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 11:23:17.140: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive +** Message: 18:53:22.312: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] +** Message: 18:53:22.312: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 18:53:22.312: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 11:23:17.261: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] -** Message: 11:23:17.264: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] -** Message: 11:23:17.265: Compiling codegen: +** Message: 18:53:22.347: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] +** Message: 18:53:22.350: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] +** Message: 18:53:22.354: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c -** Message: 11:23:18.480: Compiling codegen: +** Message: 18:53:24.758: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c -** Message: 11:23:19.898: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] -** Message: 11:23:19.898: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive +** Message: 18:53:28.593: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] +** Message: 18:53:28.594: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -** Message: 11:23:19.951: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] -** Message: 11:23:19.951: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] -** Message: 11:23:19.951: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive +** Message: 18:53:28.616: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] +** Message: 18:53:28.616: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] +** Message: 18:53:28.616: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -** Message: 11:23:20.390: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] -** Message: 11:23:20.391: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] -** Message: 11:23:20.391: Compiling codegen: +** Message: 18:53:28.637: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] +** Message: 18:53:28.637: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] +** Message: 18:53:28.638: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c -** Message: 11:23:21.527: Compiling codegen: +** Message: 18:53:29.506: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c -** Message: 11:23:22.571: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] -** Message: 11:23:22.571: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive +** Message: 18:53:33.434: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] +** Message: 18:53:33.435: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -** Message: 11:23:22.597: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] -** Message: 11:23:22.598: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] -** Message: 11:23:22.598: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive +** Message: 18:53:33.478: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] +** Message: 18:53:33.479: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] +** Message: 18:53:33.479: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -** Message: 11:23:22.628: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] -** Message: 11:23:22.629: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] -** Message: 11:23:22.631: Compiling codegen: +** Message: 18:53:33.511: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] +** Message: 18:53:33.511: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] +** Message: 18:53:33.513: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.c -** Message: 11:23:26.372: Compiling codegen: +** Message: 18:53:38.905: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.c -** Message: 11:23:31.422: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] -** Message: 11:23:31.423: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive +** Message: 18:53:49.514: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] +** Message: 18:53:49.514: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -** Message: 11:23:31.469: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] -** Message: 11:23:31.469: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] -** Message: 11:23:31.469: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive +** Message: 18:53:49.585: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_score] +** Message: 18:53:49.585: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] +** Message: 18:53:49.585: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -** Message: 11:23:31.767: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] -** Message: 11:23:31.768: Compiling codegen: +** Message: 18:53:49.677: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_dna2dna_93__93__32_find_32_path] +** Message: 18:53:49.678: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c -** Message: 11:23:32.547: Compiling codegen: +** Message: 18:53:50.296: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c -** Message: 11:23:33.307: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] -** Message: 11:23:33.307: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive +** Message: 18:53:50.889: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] +** Message: 18:53:50.889: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -** Message: 11:23:33.395: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] -** Message: 11:23:33.395: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] -** Message: 11:23:33.395: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive +** Message: 18:53:50.949: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] +** Message: 18:53:50.949: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] +** Message: 18:53:50.949: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -** Message: 11:23:33.487: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] -** Message: 11:23:33.487: Bootstrapper processing model [affine:local:protein2protein] -** Message: 11:23:33.487: Process optimal [optimal:affine:local:protein2protein] -** Message: 11:23:33.488: Compiling codegen: +** Message: 18:53:50.987: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] +** Message: 18:53:50.988: Bootstrapper processing model [affine:local:protein2protein] +** Message: 18:53:50.988: Process optimal [optimal:affine:local:protein2protein] +** Message: 18:53:50.989: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c -** Message: 11:23:34.374: Compiling codegen: +** Message: 18:53:51.663: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c -** Message: 11:23:35.627: Compiling codegen: +** Message: 18:53:53.142: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c -** Message: 11:23:36.971: Compiling codegen: +** Message: 18:53:54.357: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c -** Message: 11:23:38.785: Compiling codegen: +** Message: 18:53:56.945: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c -** Message: 11:23:42.154: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] -** Message: 11:23:42.154: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive +** Message: 18:53:59.273: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] +** Message: 18:53:59.274: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -** Message: 11:23:42.264: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] -** Message: 11:23:42.265: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] -** Message: 11:23:42.265: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive +** Message: 18:53:59.309: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] +** Message: 18:53:59.309: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] +** Message: 18:53:59.309: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -** Message: 11:23:42.314: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] -** Message: 11:23:42.314: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] -** Message: 11:23:42.314: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive +** Message: 18:53:59.334: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] +** Message: 18:53:59.334: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] +** Message: 18:53:59.334: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -** Message: 11:23:42.358: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] -** Message: 11:23:42.358: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] -** Message: 11:23:42.358: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive +** Message: 18:53:59.639: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] +** Message: 18:53:59.639: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] +** Message: 18:53:59.640: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -** Message: 11:23:42.406: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] -** Message: 11:23:42.406: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] -** Message: 11:23:42.407: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive +** Message: 18:53:59.715: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] +** Message: 18:53:59.715: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] +** Message: 18:53:59.715: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -** Message: 11:23:42.483: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] -** Message: 11:23:42.486: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] -** Message: 11:23:42.493: Compiling codegen: +** Message: 18:53:59.778: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] +** Message: 18:53:59.781: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] +** Message: 18:53:59.783: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c -** Message: 11:23:43.556: Compiling codegen: +** Message: 18:54:01.758: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c -** Message: 11:23:45.922: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] -** Message: 11:23:45.923: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive +** Message: 18:54:05.251: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] +** Message: 18:54:05.252: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -** Message: 11:23:45.998: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] -** Message: 11:23:45.999: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] -** Message: 11:23:45.999: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive +** Message: 18:54:05.291: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] +** Message: 18:54:05.291: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] +** Message: 18:54:05.291: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -** Message: 11:23:46.057: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] -** Message: 11:23:46.058: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] -** Message: 11:23:46.063: Compiling codegen: +** Message: 18:54:05.310: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] +** Message: 18:54:05.311: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] +** Message: 18:54:05.311: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c -** Message: 11:23:47.332: Compiling codegen: +** Message: 18:54:07.147: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c -** Message: 11:23:49.262: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] -** Message: 11:23:49.263: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive +** Message: 18:54:11.269: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] +** Message: 18:54:11.269: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -** Message: 11:23:49.334: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] -** Message: 11:23:49.335: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] -** Message: 11:23:49.335: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive +** Message: 18:54:11.473: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] +** Message: 18:54:11.474: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] +** Message: 18:54:11.474: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -** Message: 11:23:49.438: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] -** Message: 11:23:49.439: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] -** Message: 11:23:49.440: Compiling codegen: +** Message: 18:54:11.693: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] +** Message: 18:54:11.693: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] +** Message: 18:54:11.695: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.c -** Message: 11:23:52.981: Compiling codegen: +** Message: 18:54:20.069: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.c -** Message: 11:23:57.923: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] -** Message: 11:23:57.923: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive +** Message: 18:54:31.545: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] +** Message: 18:54:31.545: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -** Message: 11:23:57.991: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] -** Message: 11:23:57.991: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] -** Message: 11:23:57.991: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive +** Message: 18:54:31.650: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_score] +** Message: 18:54:31.650: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] +** Message: 18:54:31.650: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -** Message: 11:23:58.053: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] -** Message: 11:23:58.054: Compiling codegen: +** Message: 18:54:31.721: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_affine_58_local_58_protein2protein_93__93__32_find_32_path] +** Message: 18:54:31.723: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c -** Message: 11:23:58.737: Compiling codegen: +** Message: 18:54:32.820: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c -** Message: 11:23:59.439: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] -** Message: 11:23:59.439: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive +** Message: 18:54:33.250: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] +** Message: 18:54:33.250: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -** Message: 11:23:59.502: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] -** Message: 11:23:59.502: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] -** Message: 11:23:59.502: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive +** Message: 18:54:33.276: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] +** Message: 18:54:33.276: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] +** Message: 18:54:33.276: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -** Message: 11:23:59.634: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] -** Message: 11:23:59.634: Processing model [a:o] -** Message: 11:23:59.635: Bootstrapper processing model [affine:overlap:dna2dna] -** Message: 11:23:59.635: Process optimal [optimal:affine:overlap:dna2dna] -** Message: 11:23:59.636: Compiling codegen: +** Message: 18:54:33.296: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] +** Message: 18:54:33.296: Processing model [a:o] +** Message: 18:54:33.297: Bootstrapper processing model [affine:overlap:dna2dna] +** Message: 18:54:33.297: Process optimal [optimal:affine:overlap:dna2dna] +** Message: 18:54:33.298: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c -** Message: 11:24:02.284: Compiling codegen: +** Message: 18:54:35.071: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c -** Message: 11:24:04.772: Compiling codegen: +** Message: 18:54:39.746: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c -** Message: 11:24:07.100: Compiling codegen: +** Message: 18:54:44.364: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c -** Message: 11:24:08.559: Compiling codegen: +** Message: 18:54:45.822: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 11:24:10.078: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] -** Message: 11:24:10.078: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive +** Message: 18:54:52.478: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] +** Message: 18:54:52.478: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -** Message: 11:24:10.279: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] -** Message: 11:24:10.280: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] -** Message: 11:24:10.280: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive +** Message: 18:54:52.696: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] +** Message: 18:54:52.696: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] +** Message: 18:54:52.696: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -** Message: 11:24:10.330: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] -** Message: 11:24:10.331: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] -** Message: 11:24:10.331: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive +** Message: 18:54:53.020: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] +** Message: 18:54:53.020: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] +** Message: 18:54:53.020: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -** Message: 11:24:10.371: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] -** Message: 11:24:10.371: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] -** Message: 11:24:10.371: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 18:54:53.315: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] +** Message: 18:54:53.315: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] +** Message: 18:54:53.315: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -** Message: 11:24:10.501: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] -** Message: 11:24:10.501: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 11:24:10.501: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive +** Message: 18:54:54.293: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] +** Message: 18:54:54.294: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 18:54:54.294: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 11:24:10.583: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] -** Message: 11:24:10.583: Processing model [e2g] -** Message: 11:24:10.584: Bootstrapper processing model [est2genome] -** Message: 11:24:10.584: Process optimal [optimal:est2genome] -** Message: 11:24:10.586: Compiling codegen: +** Message: 18:54:54.495: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] +** Message: 18:54:54.495: Processing model [e2g] +** Message: 18:54:54.496: Bootstrapper processing model [est2genome] +** Message: 18:54:54.496: Process optimal [optimal:est2genome] +** Message: 18:54:54.497: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.c -** Message: 11:24:13.223: Compiling codegen: +** Message: 18:54:57.439: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.c -** Message: 11:24:16.444: Compiling codegen: +** Message: 18:55:07.897: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.c -** Message: 11:24:19.918: Compiling codegen: +** Message: 18:55:14.071: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.c -** Message: 11:24:27.298: Compiling codegen: +** Message: 18:55:29.899: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.c -** Message: 11:24:37.044: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] -** Message: 11:24:37.045: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] to archive +** Message: 18:56:02.542: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] +** Message: 18:56:02.542: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o -** Message: 11:24:37.312: Adding function [optimal_58_est2genome_32_find_32_score] -** Message: 11:24:37.312: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] -** Message: 11:24:37.312: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] to archive +** Message: 18:56:02.640: Adding function [optimal_58_est2genome_32_find_32_score] +** Message: 18:56:02.641: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] +** Message: 18:56:02.641: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o -** Message: 11:24:37.623: Adding function [optimal_58_est2genome_32_find_32_path] -** Message: 11:24:37.623: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] -** Message: 11:24:37.623: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] to archive +** Message: 18:56:02.846: Adding function [optimal_58_est2genome_32_find_32_path] +** Message: 18:56:02.846: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] +** Message: 18:56:02.847: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o -** Message: 11:24:37.952: Adding function [optimal_58_est2genome_32_find_32_region] -** Message: 11:24:37.953: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] -** Message: 11:24:37.953: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] to archive +** Message: 18:56:03.029: Adding function [optimal_58_est2genome_32_find_32_region] +** Message: 18:56:03.029: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] +** Message: 18:56:03.029: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o -** Message: 11:24:38.412: Adding function [optimal_58_est2genome_32_find_32_checkpoint] -** Message: 11:24:38.413: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] -** Message: 11:24:38.413: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive +** Message: 18:56:03.243: Adding function [optimal_58_est2genome_32_find_32_checkpoint] +** Message: 18:56:03.243: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] +** Message: 18:56:03.243: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o -** Message: 11:24:38.642: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] -** Message: 11:24:38.651: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] -** Message: 11:24:38.804: Compiling codegen: +** Message: 18:56:03.297: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] +** Message: 18:56:03.354: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] +** Message: 18:56:03.355: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c -** Message: 11:24:41.511: Compiling codegen: +** Message: 18:56:14.771: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:24:45.933: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] -** Message: 11:24:45.933: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive +** Message: 18:56:36.808: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] +** Message: 18:56:36.808: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -** Message: 11:24:46.018: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] -** Message: 11:24:46.019: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:24:46.020: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:56:37.106: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] +** Message: 18:56:37.106: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:56:37.106: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:24:46.201: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:24:46.201: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] -** Message: 11:24:46.203: Compiling codegen: +** Message: 18:56:37.578: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:56:37.578: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] +** Message: 18:56:37.579: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c -** Message: 11:24:48.903: Compiling codegen: +** Message: 18:56:42.683: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:24:52.610: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] -** Message: 11:24:52.610: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive +** Message: 18:56:50.117: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] +** Message: 18:56:50.118: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -** Message: 11:24:52.690: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] -** Message: 11:24:52.691: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:24:52.691: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:56:50.176: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] +** Message: 18:56:50.176: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:56:50.177: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:24:52.782: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:24:52.783: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] -** Message: 11:24:52.786: Compiling codegen: +** Message: 18:56:50.240: Adding function [Terminal_32__91_Segment_40__34_match_32_reverse_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:56:50.240: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] +** Message: 18:56:50.243: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c -** Message: 11:24:56.976: Compiling codegen: +** Message: 18:56:55.759: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:25:01.463: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] -** Message: 11:25:01.463: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive +** Message: 18:57:11.121: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] +** Message: 18:57:11.122: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -** Message: 11:25:01.512: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] -** Message: 11:25:01.513: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:25:01.513: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:57:11.201: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] +** Message: 18:57:11.201: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:57:11.201: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:25:01.571: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:25:01.571: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] -** Message: 11:25:01.573: Compiling codegen: +** Message: 18:57:11.258: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:57:11.260: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] +** Message: 18:57:11.263: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.c -** Message: 11:25:04.579: Compiling codegen: +** Message: 18:57:14.693: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:25:09.386: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] -** Message: 11:25:09.387: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive +** Message: 18:57:18.262: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] +** Message: 18:57:18.263: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score.o -** Message: 11:25:09.451: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] -** Message: 11:25:09.451: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:25:09.451: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:57:18.330: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_score] +** Message: 18:57:18.330: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:57:18.330: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:25:09.602: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:25:09.603: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] -** Message: 11:25:09.607: Compiling codegen: +** Message: 18:57:18.394: Adding function [Terminal_32__91_Segment_40__34_match_32_forward_34__45__62__34_END_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:57:18.394: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] +** Message: 18:57:18.398: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c -** Message: 11:25:18.638: Compiling codegen: +** Message: 18:57:27.721: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:25:32.043: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] -** Message: 11:25:32.043: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive +** Message: 18:57:47.689: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] +** Message: 18:57:47.689: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -** Message: 11:25:32.094: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] -** Message: 11:25:32.094: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:25:32.094: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:57:47.750: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] +** Message: 18:57:47.750: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:57:47.750: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:25:32.162: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:25:32.162: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] -** Message: 11:25:32.164: Compiling codegen: +** Message: 18:57:47.801: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:57:47.801: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] +** Message: 18:57:47.803: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c -** Message: 11:25:37.936: Compiling codegen: +** Message: 18:57:51.667: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:25:48.575: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] -** Message: 11:25:48.576: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive +** Message: 18:57:59.706: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] +** Message: 18:57:59.706: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -** Message: 11:25:48.746: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] -** Message: 11:25:48.747: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:25:48.747: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:57:59.746: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] +** Message: 18:57:59.747: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:57:59.747: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:25:48.874: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:25:48.875: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] -** Message: 11:25:48.892: Compiling codegen: +** Message: 18:57:59.873: Adding function [Src_32_span_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:57:59.874: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] +** Message: 18:57:59.877: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:26:13.762: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:26:13.762: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:58:21.367: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:58:21.368: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:26:13.906: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:26:13.907: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] -** Message: 11:26:13.909: Compiling codegen: +** Message: 18:58:21.442: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_reverse_34__45__62__34_intron_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:58:21.442: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] +** Message: 18:58:21.444: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.c -** Message: 11:26:21.989: Compiling codegen: +** Message: 18:58:30.958: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:26:30.734: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] -** Message: 11:26:30.734: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive +** Message: 18:58:42.865: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] +** Message: 18:58:42.865: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score.o -** Message: 11:26:31.427: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] -** Message: 11:26:31.427: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:26:31.428: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:58:42.973: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_score] +** Message: 18:58:42.973: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:58:42.973: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:26:31.684: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:26:31.684: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] -** Message: 11:26:31.692: Compiling codegen: +** Message: 18:58:43.041: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_reverse_34__45__62__34_match_32_reverse_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:58:43.041: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] +** Message: 18:58:43.044: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c -** Message: 11:26:41.719: Compiling codegen: +** Message: 18:58:54.148: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:26:51.955: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] -** Message: 11:26:51.955: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive +** Message: 18:59:10.696: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] +** Message: 18:59:10.697: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -** Message: 11:26:52.120: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] -** Message: 11:26:52.121: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:26:52.121: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:59:10.724: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] +** Message: 18:59:10.724: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:59:10.724: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:26:52.197: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:26:52.197: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] -** Message: 11:26:52.199: Compiling codegen: +** Message: 18:59:10.749: Adding function [HeuristicJoin_58__91_Segment_40__34_match_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:59:10.749: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] +** Message: 18:59:10.751: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c -** Message: 11:26:54.643: Compiling codegen: +** Message: 18:59:13.047: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:26:58.701: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] -** Message: 11:26:58.701: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive +** Message: 18:59:23.116: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] +** Message: 18:59:23.117: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -** Message: 11:26:58.774: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] -** Message: 11:26:58.775: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:26:58.775: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:59:23.552: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] +** Message: 18:59:23.552: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:59:23.552: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:26:58.875: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:26:58.875: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] -** Message: 11:26:58.887: Compiling codegen: +** Message: 18:59:24.049: Adding function [Src_32_span_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:59:24.049: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] +** Message: 18:59:24.052: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:27:07.394: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:27:07.395: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:59:42.805: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:59:42.805: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:27:07.450: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:27:07.451: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] -** Message: 11:27:07.453: Compiling codegen: +** Message: 18:59:43.867: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_32_forward_34__45__62__34_intron_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:59:43.867: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] +** Message: 18:59:43.869: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.c -** Message: 11:27:11.146: Compiling codegen: +** Message: 18:59:47.316: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.c -** Message: 11:27:16.596: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] -** Message: 11:27:16.596: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive +** Message: 18:59:55.025: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] +** Message: 18:59:55.025: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score.o -** Message: 11:27:17.282: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] -** Message: 11:27:17.282: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] -** Message: 11:27:17.282: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive +** Message: 18:59:55.569: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_score] +** Message: 18:59:55.569: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] +** Message: 18:59:55.569: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path.o -** Message: 11:27:17.648: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] -** Message: 11:27:17.650: Compiling codegen: +** Message: 18:59:56.283: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_forward_34__45__62__34_match_32_forward_34__41__58__91_est2genome_93__93__32_find_32_path] +** Message: 18:59:56.285: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c -** Message: 11:27:18.523: Compiling codegen: +** Message: 18:59:57.499: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c -** Message: 11:27:19.476: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] -** Message: 11:27:19.477: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive +** Message: 18:59:58.995: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] +** Message: 18:59:58.996: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -** Message: 11:27:19.574: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] -** Message: 11:27:19.574: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] -** Message: 11:27:19.574: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive +** Message: 18:59:59.518: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] +** Message: 18:59:59.519: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] +** Message: 18:59:59.519: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -** Message: 11:27:19.644: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] -** Message: 11:27:19.645: Processing model [ner] -** Message: 11:27:19.645: Bootstrapper processing model [NER:affine:local:dna2dna] -** Message: 11:27:19.645: Process optimal [optimal:NER:affine:local:dna2dna] -** Message: 11:27:19.646: Compiling codegen: +** Message: 19:00:00.310: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] +** Message: 19:00:00.311: Processing model [ner] +** Message: 19:00:00.312: Bootstrapper processing model [NER:affine:local:dna2dna] +** Message: 19:00:00.312: Process optimal [optimal:NER:affine:local:dna2dna] +** Message: 19:00:00.312: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c -** Message: 11:27:20.309: Compiling codegen: +** Message: 19:00:01.168: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c -** Message: 11:27:21.350: Compiling codegen: +** Message: 19:00:02.900: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c -** Message: 11:27:22.497: Compiling codegen: +** Message: 19:00:04.379: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c -** Message: 11:27:24.256: Compiling codegen: +** Message: 19:00:05.953: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 11:27:26.982: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] -** Message: 11:27:26.983: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive +** Message: 19:00:08.199: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] +** Message: 19:00:08.199: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -** Message: 11:27:27.443: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] -** Message: 11:27:27.443: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] -** Message: 11:27:27.443: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive +** Message: 19:00:08.356: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] +** Message: 19:00:08.357: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] +** Message: 19:00:08.357: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -** Message: 11:27:27.921: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] -** Message: 11:27:27.921: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] -** Message: 11:27:27.922: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive +** Message: 19:00:08.523: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] +** Message: 19:00:08.523: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] +** Message: 19:00:08.523: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -** Message: 11:27:28.342: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] -** Message: 11:27:28.342: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] -** Message: 11:27:28.342: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 19:00:09.039: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] +** Message: 19:00:09.040: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] +** Message: 19:00:09.040: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -** Message: 11:27:28.465: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] -** Message: 11:27:28.466: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 11:27:28.466: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive +** Message: 19:00:10.466: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] +** Message: 19:00:10.466: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 19:00:10.466: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 11:27:28.610: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] -** Message: 11:27:28.615: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] -** Message: 11:27:28.617: Compiling codegen: +** Message: 19:00:10.878: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] +** Message: 19:00:10.888: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] +** Message: 19:00:10.889: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c -** Message: 11:27:30.432: Compiling codegen: +** Message: 19:00:13.376: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c -** Message: 11:27:32.607: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] -** Message: 11:27:32.608: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive +** Message: 19:00:16.949: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] +** Message: 19:00:16.949: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -** Message: 11:27:32.829: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] -** Message: 11:27:32.829: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] -** Message: 11:27:32.829: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive +** Message: 19:00:17.849: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] +** Message: 19:00:17.849: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] +** Message: 19:00:17.850: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -** Message: 11:27:33.303: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] -** Message: 11:27:33.303: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] -** Message: 11:27:33.304: Compiling codegen: +** Message: 19:00:18.419: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] +** Message: 19:00:18.419: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] +** Message: 19:00:18.420: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c -** Message: 11:27:34.395: Compiling codegen: +** Message: 19:00:20.074: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c -** Message: 11:27:36.080: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] -** Message: 11:27:36.081: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive +** Message: 19:00:21.950: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] +** Message: 19:00:21.950: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -** Message: 11:27:36.184: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] -** Message: 11:27:36.185: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] -** Message: 11:27:36.185: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive +** Message: 19:00:22.197: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] +** Message: 19:00:22.197: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] +** Message: 19:00:22.197: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -** Message: 11:27:36.291: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] -** Message: 11:27:36.292: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] -** Message: 11:27:36.294: Compiling codegen: +** Message: 19:00:22.627: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] +** Message: 19:00:22.627: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] +** Message: 19:00:22.629: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c -** Message: 11:27:39.723: Compiling codegen: +** Message: 19:00:27.140: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c -** Message: 11:27:45.829: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] -** Message: 11:27:45.830: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive +** Message: 19:00:32.377: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] +** Message: 19:00:32.377: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -** Message: 11:27:45.918: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] -** Message: 11:27:45.919: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] -** Message: 11:27:45.919: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive +** Message: 19:00:32.894: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] +** Message: 19:00:32.894: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] +** Message: 19:00:32.894: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -** Message: 11:27:46.216: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] -** Message: 11:27:46.216: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] -** Message: 11:27:46.217: Compiling codegen: +** Message: 19:00:33.545: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] +** Message: 19:00:33.545: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] +** Message: 19:00:33.546: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c -** Message: 11:27:47.844: Compiling codegen: +** Message: 19:00:35.559: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c -** Message: 11:27:49.960: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] -** Message: 11:27:49.960: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive +** Message: 19:00:38.481: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] +** Message: 19:00:38.481: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -** Message: 11:27:50.334: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] -** Message: 11:27:50.334: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] -** Message: 11:27:50.335: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive +** Message: 19:00:38.574: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] +** Message: 19:00:38.575: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] +** Message: 19:00:38.575: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -** Message: 11:27:50.526: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] -** Message: 11:27:50.526: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] -** Message: 11:27:50.669: Compiling codegen: +** Message: 19:00:38.881: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] +** Message: 19:00:38.881: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] +** Message: 19:00:38.884: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c -** Message: 11:27:57.543: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] -** Message: 11:27:57.544: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive +** Message: 19:00:46.112: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] +** Message: 19:00:46.112: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -** Message: 11:27:58.160: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] -** Message: 11:27:58.160: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] -** Message: 11:27:58.161: Compiling codegen: +** Message: 19:00:46.752: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] +** Message: 19:00:46.752: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] +** Message: 19:00:46.754: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.c -** Message: 11:27:59.718: Compiling codegen: +** Message: 19:00:49.352: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.c -** Message: 11:28:03.490: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] -** Message: 11:28:03.491: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive +** Message: 19:00:54.002: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] +** Message: 19:00:54.002: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score.o -** Message: 11:28:03.734: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] -** Message: 11:28:03.735: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] -** Message: 11:28:03.735: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive +** Message: 19:00:54.799: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_score] +** Message: 19:00:54.799: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] +** Message: 19:00:54.799: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path.o -** Message: 11:28:03.923: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] -** Message: 11:28:03.924: Compiling codegen: +** Message: 19:00:55.943: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_dna2dna_93__93__32_find_32_path] +** Message: 19:00:55.943: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c -** Message: 11:28:04.731: Compiling codegen: +** Message: 19:00:58.002: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c -** Message: 11:28:05.422: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] -** Message: 11:28:05.423: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] to archive +** Message: 19:00:59.616: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] +** Message: 19:00:59.617: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -** Message: 11:28:05.739: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] -** Message: 11:28:05.739: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] -** Message: 11:28:05.739: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] to archive +** Message: 19:01:00.380: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] +** Message: 19:01:00.380: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] +** Message: 19:01:00.380: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -** Message: 11:28:06.030: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] -** Message: 11:28:06.031: Bootstrapper processing model [NER:affine:local:protein2protein] -** Message: 11:28:06.031: Process optimal [optimal:NER:affine:local:protein2protein] -** Message: 11:28:06.036: Compiling codegen: +** Message: 19:01:00.743: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] +** Message: 19:01:00.744: Bootstrapper processing model [NER:affine:local:protein2protein] +** Message: 19:01:00.744: Process optimal [optimal:NER:affine:local:protein2protein] +** Message: 19:01:00.745: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c -** Message: 11:28:07.135: Compiling codegen: +** Message: 19:01:01.753: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c -** Message: 11:28:08.094: Compiling codegen: +** Message: 19:01:02.742: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c -** Message: 11:28:08.902: Compiling codegen: +** Message: 19:01:04.347: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c -** Message: 11:28:10.730: Compiling codegen: +** Message: 19:01:07.543: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c -** Message: 11:28:13.024: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] -** Message: 11:28:13.024: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive +** Message: 19:01:09.671: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] +** Message: 19:01:09.671: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -** Message: 11:28:13.232: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] -** Message: 11:28:13.232: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] -** Message: 11:28:13.232: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive +** Message: 19:01:10.056: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] +** Message: 19:01:10.056: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] +** Message: 19:01:10.056: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -** Message: 11:28:13.308: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] -** Message: 11:28:13.308: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] -** Message: 11:28:13.308: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive +** Message: 19:01:10.545: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] +** Message: 19:01:10.546: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] +** Message: 19:01:10.546: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -** Message: 11:28:13.787: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] -** Message: 11:28:13.788: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] -** Message: 11:28:13.788: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive +** Message: 19:01:11.560: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] +** Message: 19:01:11.560: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] +** Message: 19:01:11.560: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -** Message: 11:28:14.003: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] -** Message: 11:28:14.003: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] -** Message: 11:28:14.003: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive +** Message: 19:01:13.631: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] +** Message: 19:01:13.631: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] +** Message: 19:01:13.631: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -** Message: 11:28:14.642: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] -** Message: 11:28:14.648: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] -** Message: 11:28:14.651: Compiling codegen: +** Message: 19:01:14.596: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] +** Message: 19:01:14.601: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] +** Message: 19:01:14.610: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c -** Message: 11:28:16.485: Compiling codegen: +** Message: 19:01:16.947: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c -** Message: 11:28:20.128: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] -** Message: 11:28:20.129: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive +** Message: 19:01:20.273: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] +** Message: 19:01:20.273: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -** Message: 11:28:20.323: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] -** Message: 11:28:20.323: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] -** Message: 11:28:20.323: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive +** Message: 19:01:20.988: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] +** Message: 19:01:20.988: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] +** Message: 19:01:20.988: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -** Message: 11:28:20.502: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] -** Message: 11:28:20.502: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] -** Message: 11:28:20.504: Compiling codegen: +** Message: 19:01:21.628: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] +** Message: 19:01:21.629: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] +** Message: 19:01:21.630: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c -** Message: 11:28:22.132: Compiling codegen: +** Message: 19:01:23.335: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c -** Message: 11:28:24.786: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] -** Message: 11:28:24.787: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive +** Message: 19:01:25.214: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] +** Message: 19:01:25.214: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -** Message: 11:28:24.926: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] -** Message: 11:28:24.927: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] -** Message: 11:28:24.927: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive +** Message: 19:01:25.586: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] +** Message: 19:01:25.586: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] +** Message: 19:01:25.586: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -** Message: 11:28:25.242: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] -** Message: 11:28:25.243: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] -** Message: 11:28:25.273: Compiling codegen: +** Message: 19:01:26.435: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] +** Message: 19:01:26.435: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] +** Message: 19:01:26.437: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c -** Message: 11:28:30.153: Compiling codegen: +** Message: 19:01:30.362: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c -** Message: 11:28:38.788: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] -** Message: 11:28:38.788: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive +** Message: 19:01:38.610: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] +** Message: 19:01:38.610: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -** Message: 11:28:39.546: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] -** Message: 11:28:39.547: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] -** Message: 11:28:39.547: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive +** Message: 19:01:39.428: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] +** Message: 19:01:39.429: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] +** Message: 19:01:39.429: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -** Message: 11:28:39.694: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] -** Message: 11:28:39.695: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] -** Message: 11:28:39.696: Compiling codegen: +** Message: 19:01:40.024: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] +** Message: 19:01:40.024: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] +** Message: 19:01:40.025: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c -** Message: 11:28:42.120: Compiling codegen: +** Message: 19:01:41.681: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c -** Message: 11:28:44.794: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] -** Message: 11:28:44.795: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive +** Message: 19:01:44.049: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] +** Message: 19:01:44.050: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -** Message: 11:28:44.978: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] -** Message: 11:28:44.979: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] -** Message: 11:28:44.979: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive +** Message: 19:01:44.444: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] +** Message: 19:01:44.444: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] +** Message: 19:01:44.444: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -** Message: 11:28:45.157: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] -** Message: 11:28:45.157: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] -** Message: 11:28:45.161: Compiling codegen: +** Message: 19:01:46.573: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] +** Message: 19:01:46.573: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] +** Message: 19:01:46.576: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c -** Message: 11:28:52.082: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] -** Message: 11:28:52.082: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive +** Message: 19:02:01.892: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] +** Message: 19:02:01.892: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -** Message: 11:28:52.271: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] -** Message: 11:28:52.271: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] -** Message: 11:28:52.272: Compiling codegen: +** Message: 19:02:02.000: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_ner_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] +** Message: 19:02:02.000: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] +** Message: 19:02:02.001: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.c -** Message: 11:28:54.571: Compiling codegen: +** Message: 19:02:03.409: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.c -** Message: 11:28:58.290: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] -** Message: 11:28:58.290: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive +** Message: 19:02:06.412: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] +** Message: 19:02:06.413: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score.o -** Message: 11:28:58.442: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] -** Message: 11:28:58.442: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] -** Message: 11:28:58.443: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive +** Message: 19:02:06.705: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_score] +** Message: 19:02:06.705: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] +** Message: 19:02:06.705: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path.o -** Message: 11:28:58.565: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] -** Message: 11:28:58.567: Compiling codegen: +** Message: 19:02:07.533: Adding function [Dst_32_span_32__91_Segment_40__34_ner_34__45__62__34_match_34__41__58__91_NER_58_affine_58_local_58_protein2protein_93__93__32_find_32_path] +** Message: 19:02:07.534: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c -** Message: 11:28:59.092: Compiling codegen: +** Message: 19:02:09.783: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c -** Message: 11:28:59.894: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] -** Message: 11:28:59.894: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] to archive +** Message: 19:02:11.175: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] +** Message: 19:02:11.175: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -** Message: 11:29:00.033: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] -** Message: 11:29:00.033: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] -** Message: 11:29:00.033: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] to archive +** Message: 19:02:11.288: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] +** Message: 19:02:11.289: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] +** Message: 19:02:11.289: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -** Message: 11:29:00.118: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] -** Message: 11:29:00.119: Processing model [p2d] -** Message: 11:29:00.119: Bootstrapper processing model [protein2dna:local] -** Message: 11:29:00.120: Process optimal [optimal:protein2dna:local] -** Message: 11:29:00.120: Compiling codegen: +** Message: 19:02:11.462: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] +** Message: 19:02:11.462: Processing model [p2d] +** Message: 19:02:11.462: Bootstrapper processing model [protein2dna:local] +** Message: 19:02:11.462: Process optimal [optimal:protein2dna:local] +** Message: 19:02:11.463: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.c -** Message: 11:29:01.328: Compiling codegen: +** Message: 19:02:13.194: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.c -** Message: 11:29:03.050: Compiling codegen: +** Message: 19:02:16.762: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.c -** Message: 11:29:04.885: Compiling codegen: +** Message: 19:02:19.395: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c -** Message: 11:29:08.035: Compiling codegen: +** Message: 19:02:23.479: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c -** Message: 11:29:11.727: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] -** Message: 11:29:11.727: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive +** Message: 19:02:33.572: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] +** Message: 19:02:33.572: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o -** Message: 11:29:11.868: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] -** Message: 11:29:11.869: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] -** Message: 11:29:11.869: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive +** Message: 19:02:33.678: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] +** Message: 19:02:33.678: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] +** Message: 19:02:33.678: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o -** Message: 11:29:11.952: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] -** Message: 11:29:11.953: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] -** Message: 11:29:11.953: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive +** Message: 19:02:33.827: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] +** Message: 19:02:33.827: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] +** Message: 19:02:33.828: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o -** Message: 11:29:12.091: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] -** Message: 11:29:12.091: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] -** Message: 11:29:12.091: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive +** Message: 19:02:33.962: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] +** Message: 19:02:33.962: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] +** Message: 19:02:33.963: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -** Message: 11:29:12.183: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] -** Message: 11:29:12.183: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] -** Message: 11:29:12.183: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive +** Message: 19:02:34.341: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] +** Message: 19:02:34.341: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] +** Message: 19:02:34.341: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -** Message: 11:29:12.372: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] -** Message: 11:29:12.381: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] -** Message: 11:29:12.383: Compiling codegen: +** Message: 19:02:34.535: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] +** Message: 19:02:34.561: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] +** Message: 19:02:34.701: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c -** Message: 11:29:15.019: Compiling codegen: +** Message: 19:02:40.780: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c -** Message: 11:29:19.021: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] -** Message: 11:29:19.022: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:02:46.313: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] +** Message: 19:02:46.313: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -** Message: 11:29:19.161: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] -** Message: 11:29:19.162: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] -** Message: 11:29:19.162: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:02:46.777: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] +** Message: 19:02:46.778: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] +** Message: 19:02:46.778: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -** Message: 11:29:19.258: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] -** Message: 11:29:19.259: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] -** Message: 11:29:19.260: Compiling codegen: +** Message: 19:02:47.089: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] +** Message: 19:02:47.090: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] +** Message: 19:02:47.091: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c -** Message: 11:29:20.648: Compiling codegen: +** Message: 19:02:49.121: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c -** Message: 11:29:23.118: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] -** Message: 11:29:23.119: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:02:53.848: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] +** Message: 19:02:53.848: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -** Message: 11:29:23.219: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] -** Message: 11:29:23.219: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] -** Message: 11:29:23.219: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:02:54.454: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] +** Message: 19:02:54.455: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] +** Message: 19:02:54.455: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -** Message: 11:29:23.419: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] -** Message: 11:29:23.419: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] -** Message: 11:29:23.424: Compiling codegen: +** Message: 19:02:55.786: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] +** Message: 19:02:55.786: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] +** Message: 19:02:55.789: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.c -** Message: 11:29:28.708: Compiling codegen: +** Message: 19:03:02.308: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.c -** Message: 11:29:36.126: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] -** Message: 11:29:36.127: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:03:14.091: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] +** Message: 19:03:14.091: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score.o -** Message: 11:29:36.798: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] -** Message: 11:29:36.799: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] -** Message: 11:29:36.799: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:03:14.213: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_score] +** Message: 19:03:14.213: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] +** Message: 19:03:14.213: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path.o -** Message: 11:29:37.293: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] -** Message: 11:29:37.294: Compiling codegen: +** Message: 19:03:14.330: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2dna_58_local_93__93__32_find_32_path] +** Message: 19:03:14.331: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c -** Message: 11:29:38.005: Compiling codegen: +** Message: 19:03:15.230: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c -** Message: 11:29:38.646: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] -** Message: 11:29:38.646: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive +** Message: 19:03:15.681: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] +** Message: 19:03:15.681: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -** Message: 11:29:38.890: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] -** Message: 11:29:38.891: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] -** Message: 11:29:38.891: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive +** Message: 19:03:15.761: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] +** Message: 19:03:15.761: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] +** Message: 19:03:15.761: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -** Message: 11:29:39.255: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] -** Message: 11:29:39.255: Processing model [p2d:b] -** Message: 11:29:39.256: Bootstrapper processing model [protein2dna:bestfit] -** Message: 11:29:39.256: Process optimal [optimal:protein2dna:bestfit] -** Message: 11:29:39.371: Compiling codegen: +** Message: 19:03:15.889: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] +** Message: 19:03:15.890: Processing model [p2d:b] +** Message: 19:03:15.890: Bootstrapper processing model [protein2dna:bestfit] +** Message: 19:03:15.890: Process optimal [optimal:protein2dna:bestfit] +** Message: 19:03:15.893: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.c -** Message: 11:29:42.252: Compiling codegen: +** Message: 19:03:20.696: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.c -** Message: 11:29:47.639: Compiling codegen: +** Message: 19:03:26.983: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.c -** Message: 11:29:51.856: Compiling codegen: +** Message: 19:03:33.767: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c -** Message: 11:29:55.012: Compiling codegen: +** Message: 19:03:39.112: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c -** Message: 11:29:58.460: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] -** Message: 11:29:58.460: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive +** Message: 19:03:43.713: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] +** Message: 19:03:43.713: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -** Message: 11:29:58.950: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] -** Message: 11:29:58.951: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] -** Message: 11:29:58.951: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive +** Message: 19:03:43.797: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] +** Message: 19:03:43.798: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] +** Message: 19:03:43.798: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -** Message: 11:29:59.519: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] -** Message: 11:29:59.520: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] -** Message: 11:29:59.520: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive +** Message: 19:03:43.902: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] +** Message: 19:03:43.902: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] +** Message: 19:03:43.902: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -** Message: 11:29:59.700: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] -** Message: 11:29:59.700: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] -** Message: 11:29:59.700: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive +** Message: 19:03:44.012: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] +** Message: 19:03:44.012: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] +** Message: 19:03:44.012: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -** Message: 11:30:00.433: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] -** Message: 11:30:00.433: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] -** Message: 11:30:00.434: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive +** Message: 19:03:44.153: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] +** Message: 19:03:44.153: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] +** Message: 19:03:44.154: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -** Message: 11:30:00.778: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] -** Message: 11:30:00.779: Processing model [p2g] -** Message: 11:30:00.780: Bootstrapper processing model [protein2genome:local] -** Message: 11:30:00.780: Process optimal [optimal:protein2genome:local] -** Message: 11:30:00.781: Compiling codegen: +** Message: 19:03:44.305: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] +** Message: 19:03:44.305: Processing model [p2g] +** Message: 19:03:44.308: Bootstrapper processing model [protein2genome:local] +** Message: 19:03:44.309: Process optimal [optimal:protein2genome:local] +** Message: 19:03:44.310: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.c -** Message: 11:30:04.255: Compiling codegen: +** Message: 19:03:46.941: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.c -** Message: 11:30:08.397: Compiling codegen: +** Message: 19:03:53.167: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.c -** Message: 11:30:12.526: Compiling codegen: +** Message: 19:03:56.756: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c -** Message: 11:30:24.225: Compiling codegen: +** Message: 19:04:10.021: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c -** Message: 11:30:45.494: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] -** Message: 11:30:45.494: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive +** Message: 19:04:35.865: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] +** Message: 19:04:35.866: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o -** Message: 11:30:45.736: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] -** Message: 11:30:45.736: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] -** Message: 11:30:45.737: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive +** Message: 19:04:36.535: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] +** Message: 19:04:36.535: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] +** Message: 19:04:36.535: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o -** Message: 11:30:45.935: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] -** Message: 11:30:45.935: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] -** Message: 11:30:45.935: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive +** Message: 19:04:37.590: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] +** Message: 19:04:37.590: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] +** Message: 19:04:37.590: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o -** Message: 11:30:46.086: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] -** Message: 11:30:46.087: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] -** Message: 11:30:46.087: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive +** Message: 19:04:38.329: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] +** Message: 19:04:38.329: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] +** Message: 19:04:38.329: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -** Message: 11:30:46.358: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] -** Message: 11:30:46.358: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] -** Message: 11:30:46.358: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive +** Message: 19:04:38.642: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] +** Message: 19:04:38.643: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] +** Message: 19:04:38.643: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -** Message: 11:30:46.646: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] -** Message: 11:30:46.728: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] -** Message: 11:30:46.766: Compiling codegen: +** Message: 19:04:39.136: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] +** Message: 19:04:39.202: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] +** Message: 19:04:39.257: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c -** Message: 11:31:05.180: Compiling codegen: +** Message: 19:04:53.181: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:31:35.725: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] -** Message: 11:31:35.725: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:05:20.785: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] +** Message: 19:05:20.786: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -** Message: 11:31:36.079: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] -** Message: 11:31:36.079: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:31:36.079: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:05:20.935: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] +** Message: 19:05:20.935: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:05:20.935: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:31:37.134: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:31:37.135: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] -** Message: 11:31:37.138: Compiling codegen: +** Message: 19:05:21.145: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:05:21.145: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] +** Message: 19:05:21.148: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c -** Message: 11:31:43.607: Compiling codegen: +** Message: 19:05:31.618: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:31:58.679: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] -** Message: 11:31:58.679: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:05:40.621: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] +** Message: 19:05:40.621: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -** Message: 11:31:59.586: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] -** Message: 11:31:59.586: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:31:59.586: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:05:40.964: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] +** Message: 19:05:40.964: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:05:40.964: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:31:59.943: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:31:59.946: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] -** Message: 11:31:59.964: Compiling codegen: +** Message: 19:05:41.065: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:05:41.065: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] +** Message: 19:05:41.115: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c -** Message: 11:32:34.094: Compiling codegen: +** Message: 19:06:06.876: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:33:41.218: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] -** Message: 11:33:41.219: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:07:18.395: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] +** Message: 19:07:18.396: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -** Message: 11:33:41.502: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] -** Message: 11:33:41.503: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:33:41.503: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:07:18.706: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] +** Message: 19:07:18.707: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:07:18.707: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:33:42.407: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:33:42.408: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] -** Message: 11:33:42.470: Compiling codegen: +** Message: 19:07:18.977: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:07:18.978: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] +** Message: 19:07:18.985: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c -** Message: 11:33:50.997: Compiling codegen: +** Message: 19:07:27.514: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:34:00.425: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] -** Message: 11:34:00.425: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:07:39.458: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] +** Message: 19:07:39.458: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -** Message: 11:34:00.534: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] -** Message: 11:34:00.534: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:34:00.534: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:07:39.563: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] +** Message: 19:07:39.563: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:07:39.563: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:34:00.747: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:34:00.748: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] -** Message: 11:34:00.755: Compiling codegen: +** Message: 19:07:39.828: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:07:39.829: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] +** Message: 19:07:39.840: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:34:52.866: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:34:52.867: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:09:01.491: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:09:01.491: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:34:53.146: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:34:53.146: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] -** Message: 11:34:53.159: Compiling codegen: +** Message: 19:09:01.621: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_0_58_0_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:09:01.623: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] +** Message: 19:09:01.632: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c -** Message: 11:35:11.386: Compiling codegen: +** Message: 19:09:14.283: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:35:41.651: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] -** Message: 11:35:41.651: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:09:45.586: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] +** Message: 19:09:45.586: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -** Message: 11:35:42.515: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] -** Message: 11:35:42.515: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:35:42.515: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:09:45.655: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] +** Message: 19:09:45.655: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:09:45.655: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:35:43.327: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:35:43.328: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] -** Message: 11:35:43.330: Compiling codegen: +** Message: 19:09:45.760: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_0_58_0_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:09:45.760: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] +** Message: 19:09:45.764: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c -** Message: 11:35:49.311: Compiling codegen: +** Message: 19:09:55.095: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:35:58.398: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] -** Message: 11:35:58.399: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:10:08.913: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] +** Message: 19:10:08.914: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -** Message: 11:35:58.523: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] -** Message: 11:35:58.523: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:35:58.523: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:10:08.972: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] +** Message: 19:10:08.973: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:10:08.973: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:35:58.788: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:35:58.788: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] -** Message: 11:35:58.798: Compiling codegen: +** Message: 19:10:09.122: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:10:09.123: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] +** Message: 19:10:09.138: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:36:43.483: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:36:43.483: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:11:01.358: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:11:01.359: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:36:43.639: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:36:43.639: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] -** Message: 11:36:43.645: Compiling codegen: +** Message: 19:11:01.510: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_1_58_2_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:11:01.510: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] +** Message: 19:11:01.515: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c -** Message: 11:36:53.328: Compiling codegen: +** Message: 19:11:21.722: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:37:15.504: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] -** Message: 11:37:15.504: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:11:53.327: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] +** Message: 19:11:53.327: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -** Message: 11:37:15.698: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] -** Message: 11:37:15.698: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:37:15.698: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:11:53.389: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] +** Message: 19:11:53.389: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:11:53.389: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:37:16.034: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:37:16.034: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] -** Message: 11:37:16.037: Compiling codegen: +** Message: 19:11:53.483: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_1_58_2_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:11:53.483: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] +** Message: 19:11:53.487: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c -** Message: 11:37:22.573: Compiling codegen: +** Message: 19:12:04.829: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:37:32.178: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] -** Message: 11:37:32.178: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:12:17.533: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] +** Message: 19:12:17.534: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -** Message: 11:37:32.403: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] -** Message: 11:37:32.403: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:37:32.404: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:12:17.598: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] +** Message: 19:12:17.598: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:12:17.599: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:37:32.774: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:37:32.775: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] -** Message: 11:37:32.783: Compiling codegen: +** Message: 19:12:17.714: Adding function [Src_32_span_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:12:17.714: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] +** Message: 19:12:17.722: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:38:20.725: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:38:20.725: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:13:43.348: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:13:43.348: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:38:20.934: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:38:20.935: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] -** Message: 11:38:20.939: Compiling codegen: +** Message: 19:13:43.574: Adding function [Src_32_span_32_traceback_32__91_Segment_40__34_match_34__45__62__34_intron_32_2_58_1_32_phase_45_T_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:13:43.574: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] +** Message: 19:13:43.579: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.c -** Message: 11:38:35.527: Compiling codegen: +** Message: 19:14:22.760: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.c -** Message: 11:39:05.521: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] -** Message: 11:39:05.522: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive +** Message: 19:15:27.563: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] +** Message: 19:15:27.563: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score.o -** Message: 11:39:05.631: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] -** Message: 11:39:05.631: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] -** Message: 11:39:05.631: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive +** Message: 19:15:27.827: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_score] +** Message: 19:15:27.827: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] +** Message: 19:15:27.827: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path.o -** Message: 11:39:05.757: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] -** Message: 11:39:05.759: Compiling codegen: +** Message: 19:15:28.083: Adding function [Dst_32_span_32__91_Segment_40__34_intron_32_2_58_1_32_phase_45_T_34__45__62__34_match_34__41__58__91_protein2genome_58_local_93__93__32_find_32_path] +** Message: 19:15:28.084: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c -** Message: 11:39:06.458: Compiling codegen: +** Message: 19:15:30.385: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c -** Message: 11:39:07.255: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] -** Message: 11:39:07.255: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive +** Message: 19:15:31.462: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] +** Message: 19:15:31.462: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -** Message: 11:39:07.363: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] -** Message: 11:39:07.363: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] -** Message: 11:39:07.363: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive +** Message: 19:15:31.563: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] +** Message: 19:15:31.563: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] +** Message: 19:15:31.563: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -** Message: 11:39:07.475: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] -** Message: 11:39:07.476: Processing model [p2g:b] -** Message: 11:39:07.476: Bootstrapper processing model [protein2genome:bestfit] -** Message: 11:39:07.476: Process optimal [optimal:protein2genome:bestfit] -** Message: 11:39:07.482: Compiling codegen: +** Message: 19:15:31.755: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] +** Message: 19:15:31.756: Processing model [p2g:b] +** Message: 19:15:31.756: Bootstrapper processing model [protein2genome:bestfit] +** Message: 19:15:31.757: Process optimal [optimal:protein2genome:bestfit] +** Message: 19:15:31.791: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.c -** Message: 11:39:19.252: Compiling codegen: +** Message: 19:15:59.519: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.c -** Message: 11:39:45.052: Compiling codegen: +** Message: 19:16:52.034: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.c -** Message: 11:40:04.628: Compiling codegen: +** Message: 19:17:16.947: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c -** Message: 11:40:13.413: Compiling codegen: +** Message: 19:17:30.345: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c -** Message: 11:40:27.689: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] -** Message: 11:40:27.689: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive +** Message: 19:17:51.930: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] +** Message: 19:17:51.931: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -** Message: 11:40:27.811: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] -** Message: 11:40:27.811: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] -** Message: 11:40:27.812: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive +** Message: 19:17:52.176: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] +** Message: 19:17:52.176: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] +** Message: 19:17:52.176: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -** Message: 11:40:27.924: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] -** Message: 11:40:27.924: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] -** Message: 11:40:27.924: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive +** Message: 19:17:52.416: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] +** Message: 19:17:52.417: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] +** Message: 19:17:52.417: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -** Message: 11:40:28.132: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] -** Message: 11:40:28.132: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] -** Message: 11:40:28.132: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive +** Message: 19:17:52.744: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] +** Message: 19:17:52.744: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] +** Message: 19:17:52.744: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -** Message: 11:40:28.631: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] -** Message: 11:40:28.632: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] -** Message: 11:40:28.632: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive +** Message: 19:17:53.390: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] +** Message: 19:17:53.390: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] +** Message: 19:17:53.390: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -** Message: 11:40:28.790: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] -** Message: 11:40:28.791: Processing model [c2c] -** Message: 11:40:28.792: Bootstrapper processing model [coding2coding] -** Message: 11:40:28.792: Process optimal [optimal:coding2coding] -** Message: 11:40:28.794: Compiling codegen: +** Message: 19:17:54.500: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] +** Message: 19:17:54.500: Processing model [c2c] +** Message: 19:17:54.501: Bootstrapper processing model [coding2coding] +** Message: 19:17:54.501: Process optimal [optimal:coding2coding] +** Message: 19:17:54.503: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.c -** Message: 11:40:30.867: Compiling codegen: +** Message: 19:17:57.423: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.c -** Message: 11:40:33.930: Compiling codegen: +** Message: 19:18:02.563: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.c -** Message: 11:40:37.448: Compiling codegen: +** Message: 19:18:07.690: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.c -** Message: 11:40:46.011: Compiling codegen: +** Message: 19:18:19.756: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.c -** Message: 11:40:56.776: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] -** Message: 11:40:56.777: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] to archive +** Message: 19:18:33.269: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] +** Message: 19:18:33.269: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o -** Message: 11:40:56.960: Adding function [optimal_58_coding2coding_32_find_32_score] -** Message: 11:40:56.960: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] -** Message: 11:40:56.960: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] to archive +** Message: 19:18:33.365: Adding function [optimal_58_coding2coding_32_find_32_score] +** Message: 19:18:33.365: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] +** Message: 19:18:33.365: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o -** Message: 11:40:57.182: Adding function [optimal_58_coding2coding_32_find_32_path] -** Message: 11:40:57.183: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] -** Message: 11:40:57.183: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] to archive +** Message: 19:18:33.523: Adding function [optimal_58_coding2coding_32_find_32_path] +** Message: 19:18:33.523: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] +** Message: 19:18:33.523: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o -** Message: 11:40:57.384: Adding function [optimal_58_coding2coding_32_find_32_region] -** Message: 11:40:57.385: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] -** Message: 11:40:57.385: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive +** Message: 19:18:33.684: Adding function [optimal_58_coding2coding_32_find_32_region] +** Message: 19:18:33.684: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] +** Message: 19:18:33.684: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o -** Message: 11:40:57.994: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] -** Message: 11:40:57.995: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] -** Message: 11:40:57.995: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive +** Message: 19:18:34.055: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] +** Message: 19:18:34.055: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] +** Message: 19:18:34.055: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o -** Message: 11:40:58.230: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] -** Message: 11:40:58.263: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] -** Message: 11:40:58.269: Compiling codegen: +** Message: 19:18:34.423: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] +** Message: 19:18:34.477: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] +** Message: 19:18:34.486: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c -** Message: 11:41:04.513: Compiling codegen: +** Message: 19:18:42.310: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c -** Message: 11:41:14.928: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] -** Message: 11:41:14.928: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive +** Message: 19:18:56.381: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] +** Message: 19:18:56.381: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -** Message: 11:41:15.141: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score] -** Message: 11:41:15.142: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] -** Message: 11:41:15.142: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive +** Message: 19:18:56.617: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score] +** Message: 19:18:56.618: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] +** Message: 19:18:56.618: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -** Message: 11:41:15.421: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path] -** Message: 11:41:15.422: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] -** Message: 11:41:15.424: Compiling codegen: +** Message: 19:18:57.107: Adding function [Terminal_32__91_Segment_40__34_START_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path] +** Message: 19:18:57.107: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] +** Message: 19:18:57.110: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.c -** Message: 11:41:19.711: Compiling codegen: +** Message: 19:19:02.823: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.c -** Message: 11:41:24.491: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] -** Message: 11:41:24.491: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive +** Message: 19:19:09.513: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] +** Message: 19:19:09.513: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score.o -** Message: 11:41:24.808: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score] -** Message: 11:41:24.808: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] -** Message: 11:41:24.808: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive +** Message: 19:19:11.059: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_score] +** Message: 19:19:11.060: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] +** Message: 19:19:11.060: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path.o -** Message: 11:41:25.082: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path] -** Message: 11:41:25.083: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] -** Message: 11:41:25.092: Compiling codegen: +** Message: 19:19:12.989: Adding function [Terminal_32__91_Segment_40__34_match_34__45__62__34_END_34__41__58__91_coding2coding_93__93__32_find_32_path] +** Message: 19:19:12.989: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] +** Message: 19:19:13.000: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.c -** Message: 11:41:39.421: Compiling codegen: +** Message: 19:19:32.316: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.c -** Message: 11:42:02.684: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] -** Message: 11:42:02.684: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive +** Message: 19:20:22.361: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] +** Message: 19:20:22.361: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score.o -** Message: 11:42:02.885: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score] -** Message: 11:42:02.885: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] -** Message: 11:42:02.885: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive +** Message: 19:20:22.807: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_score] +** Message: 19:20:22.807: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] +** Message: 19:20:22.808: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path.o -** Message: 11:42:03.057: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path] -** Message: 11:42:03.059: Compiling codegen: +** Message: 19:20:23.524: Adding function [HeuristicJoin_58__91_Segment_40__34_match_34__45__62__34_match_34__41__58__91_coding2coding_93__93__32_find_32_path] +** Message: 19:20:23.525: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c -** Message: 11:42:03.637: Compiling codegen: +** Message: 19:20:25.222: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c -** Message: 11:42:04.334: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] -** Message: 11:42:04.336: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive +** Message: 19:20:27.182: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] +** Message: 19:20:27.182: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -** Message: 11:42:04.816: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] -** Message: 11:42:04.816: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] -** Message: 11:42:04.817: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive +** Message: 19:20:27.589: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] +** Message: 19:20:27.589: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] +** Message: 19:20:27.590: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -** Message: 11:42:05.170: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] -** Message: 11:42:05.171: Processing model [c2g] -** Message: 11:42:05.172: Bootstrapper processing model [coding2genome] -** Message: 11:42:05.172: Process optimal [optimal:coding2genome] -** Message: 11:42:05.179: Compiling codegen: +** Message: 19:20:28.010: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] +** Message: 19:20:28.010: Processing model [c2g] +** Message: 19:20:28.011: Bootstrapper processing model [coding2genome] +** Message: 19:20:28.011: Process optimal [optimal:coding2genome] +** Message: 19:20:28.017: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.c -** Message: 11:42:12.948: Compiling codegen: +** Message: 19:20:47.351: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.c -** Message: 11:42:25.403: Compiling codegen: +** Message: 19:21:11.128: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.c -** Message: 11:42:36.094: Compiling codegen: +** Message: 19:21:36.115: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.c -** Message: 11:43:06.535: Compiling codegen: +** Message: 19:22:28.061: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.c -** Message: 11:44:18.392: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] -** Message: 11:44:18.392: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] to archive +** Message: 19:25:08.799: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] +** Message: 19:25:08.800: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o -** Message: 11:44:18.655: Adding function [optimal_58_coding2genome_32_find_32_score] -** Message: 11:44:18.655: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] -** Message: 11:44:18.655: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] to archive +** Message: 19:25:09.996: Adding function [optimal_58_coding2genome_32_find_32_score] +** Message: 19:25:09.996: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] +** Message: 19:25:09.996: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o -** Message: 11:44:19.298: Adding function [optimal_58_coding2genome_32_find_32_path] -** Message: 11:44:19.298: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] -** Message: 11:44:19.298: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] to archive +** Message: 19:25:10.969: Adding function [optimal_58_coding2genome_32_find_32_path] +** Message: 19:25:10.969: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] +** Message: 19:25:10.969: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o -** Message: 11:44:19.608: Adding function [optimal_58_coding2genome_32_find_32_region] -** Message: 11:44:19.608: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] -** Message: 11:44:19.608: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive +** Message: 19:25:11.782: Adding function [optimal_58_coding2genome_32_find_32_region] +** Message: 19:25:11.783: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] +** Message: 19:25:11.783: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o -** Message: 11:44:20.182: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] -** Message: 11:44:20.183: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] -** Message: 11:44:20.183: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive +** Message: 19:25:12.794: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] +** Message: 19:25:12.794: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] +** Message: 19:25:12.794: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o -** Message: 11:44:20.543: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] -** Message: 11:44:20.544: Compiling codegen: +** Message: 19:25:13.390: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] +** Message: 19:25:13.391: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c -** Message: 11:44:21.451: Compiling codegen: +** Message: 19:25:14.718: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c -** Message: 11:44:22.668: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] -** Message: 11:44:22.669: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive +** Message: 19:25:16.668: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] +** Message: 19:25:16.669: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -** Message: 11:44:23.186: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] -** Message: 11:44:23.186: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] -** Message: 11:44:23.186: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive +** Message: 19:25:17.138: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] +** Message: 19:25:17.138: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] +** Message: 19:25:17.138: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -** Message: 11:44:23.490: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] -** Message: 11:44:23.491: Processing model [cd2g] -** Message: 11:44:23.493: Bootstrapper processing model [cdna2genome] -** Message: 11:44:23.493: Process optimal [optimal:cdna2genome] -** Message: 11:44:23.499: Compiling codegen: +** Message: 19:25:17.414: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] +** Message: 19:25:17.415: Processing model [cd2g] +** Message: 19:25:17.416: Bootstrapper processing model [cdna2genome] +** Message: 19:25:17.416: Process optimal [optimal:cdna2genome] +** Message: 19:25:17.438: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.c -** Message: 11:44:53.080: Compiling codegen: +** Message: 19:26:05.265: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.c -** Message: 11:46:12.204: Compiling codegen: +** Message: 19:28:12.866: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.c -** Message: 11:47:35.173: Compiling codegen: +** Message: 19:30:10.888: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.c -** Message: 11:52:37.567: Compiling codegen: +** Message: 19:35:09.480: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.c -** Message: 11:56:58.302: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] -** Message: 11:56:58.303: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] to archive +** Message: 19:41:06.856: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] +** Message: 19:41:06.856: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o -** Message: 11:56:58.562: Adding function [optimal_58_cdna2genome_32_find_32_score] -** Message: 11:56:58.563: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] -** Message: 11:56:58.563: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] to archive +** Message: 19:41:07.264: Adding function [optimal_58_cdna2genome_32_find_32_score] +** Message: 19:41:07.264: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] +** Message: 19:41:07.264: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o -** Message: 11:56:58.786: Adding function [optimal_58_cdna2genome_32_find_32_path] -** Message: 11:56:58.787: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] -** Message: 11:56:58.787: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] to archive +** Message: 19:41:08.079: Adding function [optimal_58_cdna2genome_32_find_32_path] +** Message: 19:41:08.079: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] +** Message: 19:41:08.079: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o -** Message: 11:56:59.082: Adding function [optimal_58_cdna2genome_32_find_32_region] -** Message: 11:56:59.082: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] -** Message: 11:56:59.082: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive +** Message: 19:41:08.927: Adding function [optimal_58_cdna2genome_32_find_32_region] +** Message: 19:41:08.927: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] +** Message: 19:41:08.927: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o -** Message: 11:56:59.328: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] -** Message: 11:56:59.329: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] -** Message: 11:56:59.329: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive +** Message: 19:41:09.366: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] +** Message: 19:41:09.366: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] +** Message: 19:41:09.366: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -** Message: 11:56:59.642: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] -** Message: 11:56:59.645: Compiling codegen: +** Message: 19:41:09.566: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] +** Message: 19:41:09.567: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c -** Message: 11:57:01.944: Compiling codegen: +** Message: 19:41:12.992: Compiling codegen: gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/build/reproducible-path/exonerate-2.4.0/src/model -I/build/reproducible-path/exonerate-2.4.0/src/comparison -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/bsdp -I/build/reproducible-path/exonerate-2.4.0/src/sdp -o /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c -** Message: 11:57:04.579: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] -** Message: 11:57:04.580: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive +** Message: 19:41:14.825: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] +** Message: 19:41:14.825: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -** Message: 11:57:04.830: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] -** Message: 11:57:04.831: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] -** Message: 11:57:04.831: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive +** Message: 19:41:15.790: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] +** Message: 19:41:15.790: Adding: [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] +** Message: 19:41:15.790: Adding object file [/build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive ar -Sq c4_model_archive.a /build/reproducible-path/exonerate-2.4.0/codegen/x86_64_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -** Message: 11:57:05.075: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] -** Message: 11:57:05.075: Compiling with: [gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -o c4_model_lookup.o -c c4_model_lookup.c] -** Message: 11:57:05.545: Adding: [c4_model_lookup.o] -** Message: 11:57:05.545: Adding object file [c4_model_lookup.o] to archive +** Message: 19:41:16.601: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] +** Message: 19:41:16.602: Compiling with: [gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/reproducible-path/exonerate-2.4.0/src/c4 -I/build/reproducible-path/exonerate-2.4.0/src/sequence -I/build/reproducible-path/exonerate-2.4.0/src/general -I/build/reproducible-path/exonerate-2.4.0/src/struct -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -o c4_model_lookup.o -c c4_model_lookup.c] +** Message: 19:41:17.153: Adding: [c4_model_lookup.o] +** Message: 19:41:17.153: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o -** Message: 11:57:05.788: Indexing archive [c4_model_archive.a] +** Message: 19:41:17.478: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a -** Message: 11:57:06.095: Done -** Message: 11:57:06.096: Finished building bootstrapping components +** Message: 19:41:17.730: Done +** Message: 19:41:17.862: Finished building bootstrapping components make all-am make[4]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src/program' gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o exonerate.o exonerate.c @@ -3027,6 +3062,23 @@ -c ../../src/sdp/scheduler.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o ipcress.o ipcress.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/comparison -I../../src/struct -I../../src/c4 -I../../src/bsdp -I../../src/sdp -I../../src/model -I../../src/hub -I../../src/general -DHOSTTYPE="\"x86_64-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/reproducible-path/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"lu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o exonerate-server.o exonerate-server.c +ipcress.c: In function 'Ipcress_prepare_PCR': +ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] + 264 | g_strup(primer_a); + | ^~~~~~~ +In file included from /usr/include/glib-2.0/glib/gstring.h:37, + from /usr/include/glib-2.0/glib/giochannel.h:36, + from /usr/include/glib-2.0/glib.h:56, + from ipcress.c:16: +/usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here + 277 | gchar* g_strup (gchar *string); + | ^~~~~~~ +ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] + 265 | g_strup(primer_b); + | ^~~~~~~ +/usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here + 277 | gchar* g_strup (gchar *string); + | ^~~~~~~ In file included from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ../../src/c4/viterbi.h:23, @@ -3048,23 +3100,6 @@ ../../src/c4/viterbi.c:965:5: note: in expansion of macro 'g_string_free' 965 | g_string_free(str, FALSE); | ^~~~~~~~~~~~~ -ipcress.c: In function 'Ipcress_prepare_PCR': -ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] - 264 | g_strup(primer_a); - | ^~~~~~~ -In file included from /usr/include/glib-2.0/glib/gstring.h:37, - from /usr/include/glib-2.0/glib/giochannel.h:36, - from /usr/include/glib-2.0/glib.h:56, - from ipcress.c:16: -/usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here - 277 | gchar* g_strup (gchar *string); - | ^~~~~~~ -ipcress.c:265:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] - 265 | g_strup(primer_b); - | ^~~~~~~ -/usr/include/glib-2.0/glib/gstrfuncs.h:277:23: note: declared here - 277 | gchar* g_strup (gchar *string); - | ^~~~~~~ exonerate-server.c: In function 'Exonerate_Server_get_hsps': exonerate-server.c:349:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" 349 | g_string_sprintfa(str, "hspset: %d", index_hsp_set->target_id); @@ -3122,6 +3157,11 @@ gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasubseq.o fastasubseq.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastatranslate.o fastatranslate.c gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastavalidcds.o fastavalidcds.c +gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fasta2esd.o fasta2esd.c +gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaannotatecdna.o fastaannotatecdna.c +gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o esd2esi.o esd2esi.c +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastachecksum fastachecksum.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasoftmask fastasoftmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 fastadiff.c: In function 'fasta_diff': fastadiff.c:70:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 70 | comp = g_strcasecmp; @@ -3134,26 +3174,36 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ -gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fasta2esd.o fasta2esd.c -gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaannotatecdna.o fastaannotatecdna.c -gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I../../src/sequence -I../../src/database -I../../src/struct -I../../src/comparison -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o esd2esi.o esd2esi.c -fastaremove.c: In function 'Argument_main': -fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] - 73 | if(!g_strcasecmp(remove_path, "stdin")){ +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastahardmask fastahardmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastareformat fastareformat.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaclean fastaclean.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaexplode fastaexplode.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaclip fastaclip.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +fastasort.c: In function 'SortKey_Mask_create': +fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] + 130 | if(!g_strcasecmp(sort_key, "id")) | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ../../src/general/argument.h:26, - from fastaremove.c:19: + from fastasort.c:20: +/usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here + 268 | gint g_strcasecmp (const gchar *s1, + | ^~~~~~~~~~~~ +fastasort.c:132:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] + 132 | else if(!g_strcasecmp(sort_key, "len")) + | ^~~~ +/usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here + 268 | gint g_strcasecmp (const gchar *s1, + | ^~~~~~~~~~~~ +fastasort.c:134:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] + 134 | else if(!g_strcasecmp(sort_key, "seq")) + | ^~~~ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaclip fastaclip.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastachecksum fastachecksum.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastacomposition fastacomposition.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 fastafetch.c: In function 'get_query_list': -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastahardmask fastahardmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 121 | if(!g_strcasecmp(query, "stdin")){ | ^~ @@ -3165,36 +3215,20 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaindex fastaindex.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -fastasort.c: In function 'SortKey_Mask_create': -fastasort.c:130:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] - 130 | if(!g_strcasecmp(sort_key, "id")) +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastacomposition fastacomposition.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +fastaremove.c: In function 'Argument_main': +fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] + 73 | if(!g_strcasecmp(remove_path, "stdin")){ | ^~ In file included from /usr/include/glib-2.0/glib/gstring.h:37, from /usr/include/glib-2.0/glib/giochannel.h:36, from /usr/include/glib-2.0/glib.h:56, from ../../src/general/argument.h:26, - from fastasort.c:20: -/usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here - 268 | gint g_strcasecmp (const gchar *s1, - | ^~~~~~~~~~~~ -fastasort.c:132:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] - 132 | else if(!g_strcasecmp(sort_key, "len")) - | ^~~~ -/usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here - 268 | gint g_strcasecmp (const gchar *s1, - | ^~~~~~~~~~~~ -fastasort.c:134:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] - 134 | else if(!g_strcasecmp(sort_key, "seq")) - | ^~~~ + from fastaremove.c:19: /usr/include/glib-2.0/glib/gstrfuncs.h:268:23: note: declared here 268 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastalength fastalength.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaoverlap fastaoverlap.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastareformat fastareformat.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaremove fastaremove.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastarevcomp fastarevcomp.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fasta2esd fasta2esd.o ../../src/database/dataset.o ../../src/struct/bitarray.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 fastasplit.c: In function 'Argument_main': fastasplit.c:92:13: warning: 'g_basename' is deprecated: Use 'g_path_get_basename' instead [-Wdeprecated-declarations] 92 | output_dir, G_DIR_SEPARATOR, g_basename(query_path)); @@ -3205,20 +3239,21 @@ /usr/include/glib-2.0/glib/gfileutils.h:207:14: note: declared here 207 | const gchar *g_basename (const gchar *file_name); | ^~~~~~~~~~ -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaclean fastaclean.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastadiff fastadiff.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaexplode fastaexplode.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaoverlap fastaoverlap.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastalength fastalength.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastarevcomp fastarevcomp.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastatranslate fastatranslate.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaindex fastaindex.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasubseq fastasubseq.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastanrdb fastanrdb.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasoftmask fastasoftmask.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fasta2esd fasta2esd.o ../../src/database/dataset.o ../../src/struct/bitarray.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasplit fastasplit.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o esd2esi esd2esi.o ../../src/database/dataset.o ../../src/database/index.o ../../src/general/threadref.o ../../src/struct/bitarray.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/struct/noitree.o ../../src/struct/splaytree.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastadiff fastadiff.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasplit fastasplit.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaannotatecdna fastaannotatecdna.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastafetch fastafetch.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastaremove fastaremove.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastavalidcds fastavalidcds.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastasort fastasort.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastatranslate fastatranslate.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 -gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastafetch fastafetch.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 +gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/exonerate-2.4.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -Wl,-z,relro -Wl,-z,now -lgthread-2.0 -pthread -lglib-2.0 -lpthread -o fastanrdb fastanrdb.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/database/fastadb.o ../../src/general/argument.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o -lm -lglib-2.0 make[3]: Leaving directory '/build/reproducible-path/exonerate-2.4.0/src/util' make[3]: Entering directory '/build/reproducible-path/exonerate-2.4.0/src' make[3]: Nothing to be done for 'all-am'. @@ -3363,7 +3398,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/exonerate/ - make -j20 install DESTDIR=/build/reproducible-path/exonerate-2.4.0/debian/exonerate AM_UPDATE_INFO_DIR=no + make -j42 install DESTDIR=/build/reproducible-path/exonerate-2.4.0/debian/exonerate AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/exonerate-2.4.0' Making install in doc make[2]: Entering directory '/build/reproducible-path/exonerate-2.4.0/doc' @@ -3591,12 +3626,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2391872/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2391872/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/308189 and its subdirectories -I: Current time: Sun Apr 28 11:57:30 -12 2024 -I: pbuilder-time-stamp: 1714348650 +I: removing directory /srv/workspace/pbuilder/2391872 and its subdirectories +I: Current time: Sun Jun 1 19:41:53 +14 2025 +I: pbuilder-time-stamp: 1748756513