Diff of the two buildlogs: -- --- b1/build.log 2023-06-09 02:56:16.602195321 +0000 +++ b2/build.log 2023-06-09 03:10:33.016711893 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jun 8 14:26:30 -12 2023 -I: pbuilder-time-stamp: 1686277590 +I: Current time: Thu Jul 11 23:19:16 +14 2024 +I: pbuilder-time-stamp: 1720689556 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./exonerate_2.4.0.orig.tar.gz] I: copying [./exonerate_2.4.0-5.debian.tar.xz] I: Extracting source -gpgv: Signature made Thu Dec 3 09:18:18 2020 -12 +gpgv: Signature made Fri Dec 4 11:18:18 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -33,137 +33,169 @@ dpkg-source: info: applying cross.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/26390/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/52864/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +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 Jul 11 23:19 /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/52864/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/52864/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='i386' + 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]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='782f00b4000f4cad83bafc9cc161e350' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='26390' - PS1='# ' - PS2='> ' + INVOCATION_ID=e788809a4cb94c88822bcb94902dc149 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=52864 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.Jxmrb7bT/pbuilderrc_B6dP --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Jxmrb7bT/b1 --logfile b1/build.log exonerate_2.4.0-5.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.Jxmrb7bT/pbuilderrc_pz4t --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Jxmrb7bT/b2 --logfile b2/build.log --extrapackages usrmerge exonerate_2.4.0-5.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos2-i386 5.10.0-23-686-pae #1 SMP Debian 5.10.179-1 (2023-05-12) i686 GNU/Linux + Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 6036 - -rwxr-xr-x 1 root root 1408088 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 22:20 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 22:20 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 20:38 fusermount - -rwxr-xr-x 1 root root 218680 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 23:43 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 22:20 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 22:20 more - -rwsr-xr-x 1 root root 58912 Mar 22 22:20 mount - -rwxr-xr-x 1 root root 13856 Mar 22 22:20 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 22:20 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 598456 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 20:38 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 22:20 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 22:20 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/26390/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Apr 24 2023 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 2023 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 218680 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 2023 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 2023 more + -rwsr-xr-x 1 root root 58912 Mar 24 2023 mount + -rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jul 11 23:19 sh -> /bin/bash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 2023 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 598456 Apr 7 2023 tar + -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 2023 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/52864/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -269,7 +301,7 @@ Get: 64 http://deb.debian.org/debian bookworm/main i386 libncurses6 i386 6.4-4 [111 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 libncurses-dev i386 6.4-4 [379 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 libreadline-dev i386 8.2-1.3 [164 kB] -Fetched 33.5 MB in 1s (23.1 MB/s) +Fetched 33.5 MB in 0s (89.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 19599 files and directories currently installed.) @@ -550,8 +582,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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/52864/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/52864/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/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 @@ -621,7 +664,7 @@ ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes @@ -650,8 +693,8 @@ checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for limits.h... yes checking for errno.h... yes checking for math.h... yes @@ -709,7 +752,7 @@ config.status: creating test/data/protein/Makefile config.status: executing depfiles commands dh_auto_build - make -j8 + make -j15 make[1]: Entering directory '/build/exonerate-2.4.0' Making all in doc make[2]: Entering directory '/build/exonerate-2.4.0/doc' @@ -765,24 +808,24 @@ 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="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 bitarray.c: In function 'BitArray_read_int': 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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/exonerate-2.4.0/src/struct' @@ -797,6 +840,22 @@ 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/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o socket.test.o socket.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/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o socket.o socket.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/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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.test.o jobqueue.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/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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:114, + 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])) @@ -842,22 +901,7 @@ /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. -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -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:114, - 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 -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/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -I../../src/struct -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 +gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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); @@ -866,11 +910,10 @@ 169 | g_string_sprintfa(full_msg, "%s", msg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 +gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 make[3]: Leaving directory '/build/exonerate-2.4.0/src/general' Making all in sequence make[3]: Entering directory '/build/exonerate-2.4.0/src/sequence' @@ -882,16 +925,10 @@ 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o submat.test.o submat.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o submat.o submat.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o translate.test.o translate.test.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:94, - 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, - | ^~~~~~~~~~~~~~~ +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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splice.test.o splice.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 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])) @@ -914,6 +951,16 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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:94, + 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")) @@ -938,15 +985,11 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o splice.test.o splice.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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/exonerate-2.4.0/src/sequence' Making all in comparison @@ -959,6 +1002,10 @@ 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/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o pcr.test.o pcr.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/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o pcr.o pcr.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/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o comparison.test.o comparison.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/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o comparison.o comparison.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/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o match.test.o match.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/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o seeder.test.o seeder.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/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o seeder.o seeder.c pcr.c: In function 'PCR_Match_allocate': pcr.c:31:9: warning: 'g_mem_chunk_alloc' is deprecated [-Wdeprecated-declarations] 31 | pcr_match = g_chunk_new(PCR_Match, pcr->match_mem_chunk); @@ -1077,10 +1124,6 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:212:23: note: declared here 212 | gchar* g_strup (gchar *string); | ^~~~~~~ -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/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o comparison.o comparison.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/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o match.test.o match.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/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o seeder.test.o seeder.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/sequence -I../../src/struct -I../../src/general -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o seeder.o seeder.c seeder.c: In function 'Seeder_decide_fsm_type': seeder.c:268:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 268 | if(!g_strcasecmp(force_fsm, "none")) @@ -1143,8 +1186,13 @@ 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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o codegen.o codegen.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o optimal.test.o optimal.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o optimal.o optimal.c -alignment.c: In function 'AlignmentView_add_SPLICE_SITE': 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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o layout.o layout.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o viterbi.o viterbi.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o subopt.o subopt.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o cgutil.o cgutil.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o layout.test.o layout.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o viterbi.test.o viterbi.test.c +alignment.c: In function 'AlignmentView_add_SPLICE_SITE': alignment.c:660:9: warning: 'g_strdown' is deprecated [-Wdeprecated-declarations] 660 | g_strdown(qy_seq_string); | ^~~~~~~~~ @@ -1185,19 +1233,14 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:212:23: note: declared here 212 | gchar* g_strup (gchar *string); | ^~~~~~~ -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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o viterbi.o viterbi.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o subopt.o subopt.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o cgutil.o cgutil.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o layout.test.o layout.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o viterbi.test.o viterbi.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o opair.test.o opair.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o opair.o opair.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o subopt.test.o subopt.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 -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -DHOSTTYPE="\"i686-pc-linux-gnu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o cgutil.test.o cgutil.test.c gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 @@ -1273,6 +1316,11 @@ 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/c4 -I../../src/bsdp -I../../src/sdp -I../../src/sequence -I../../src/general -I../../src/comparison -I../../src/struct -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DGLIB_CFLAGS="\"-I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include \"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 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)) @@ -1290,12 +1338,6 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 bootstrapper.c: In function 'Argument_main': bootstrapper.c:421:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 421 | if((!models) || (!g_strcasecmp(models, "all"))) @@ -1307,8 +1349,9 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ -gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 coding2genome.test coding2genome.test.o coding2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.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 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 cdna2genome.test cdna2genome.test.o cdna2genome.o affine.o ungapped.o frameshift.o intron.o phase.o coding2coding.o coding2genome.o est2genome.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 genome2genome.test genome2genome.test.o genome2genome.o coding2coding.o affine.o ungapped.o frameshift.o intron.o phase.o coding2genome.o cdna2genome.o est2genome.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 @@ -1324,6 +1367,38 @@ 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/general -DHOSTTYPE="\"i686-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o analysis.o analysis.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/general -DHOSTTYPE="\"i686-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bsam.o bsam.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/general -DHOSTTYPE="\"i686-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o bsam.test.o bsam.test.c +gam.c: In function 'GAM_Refinement_from_string': +gam.c:68:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] + 68 | if(!g_strcasecmp(name[i], str)) + | ^~ +In file included from /usr/include/glib-2.0/glib.h:84, + from gam.h:23, + from gam.c:21: +/usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here + 203 | gint g_strcasecmp (const gchar *s1, + | ^~~~~~~~~~~~ +gam.c: In function 'GAM_bestn_tree_destroy': +gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] + 526 | g_tree_traverse(bestn_tree, GAM_tree_collect_values, + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/glib-2.0/glib.h:94: +/usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here + 148 | void g_tree_traverse (GTree *tree, + | ^~~~~~~~~~~~~~~ +gam.c: In function 'GAM_percent_threshold_tree_destroy': +gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] + 539 | g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, + | ^~~~~~~~~~~~~~~ +/usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here + 148 | void g_tree_traverse (GTree *tree, + | ^~~~~~~~~~~~~~~ +gam.c: In function 'GAM_report': +gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] + 589 | g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, + | ^~~~~~~~~~~~~~~ +/usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here + 148 | void g_tree_traverse (GTree *tree, + | ^~~~~~~~~~~~~~~ analysis.c: In function 'Analysis_decide_scan_query': analysis.c:329:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 329 | if(!g_strcasecmp(force_scan, "none")){ @@ -1358,38 +1433,6 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | gint g_strcasecmp (const gchar *s1, | ^~~~~~~~~~~~ -gam.c: In function 'GAM_Refinement_from_string': -gam.c:68:9: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] - 68 | if(!g_strcasecmp(name[i], str)) - | ^~ -In file included from /usr/include/glib-2.0/glib.h:84, - from gam.h:23, - from gam.c:21: -/usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here - 203 | gint g_strcasecmp (const gchar *s1, - | ^~~~~~~~~~~~ -gam.c: In function 'GAM_bestn_tree_destroy': -gam.c:526:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] - 526 | g_tree_traverse(bestn_tree, GAM_tree_collect_values, - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/glib-2.0/glib.h:94: -/usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here - 148 | void g_tree_traverse (GTree *tree, - | ^~~~~~~~~~~~~~~ -gam.c: In function 'GAM_percent_threshold_tree_destroy': -gam.c:539:5: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] - 539 | g_tree_traverse(percent_threshold_tree, GAM_tree_collect_values, - | ^~~~~~~~~~~~~~~ -/usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here - 148 | void g_tree_traverse (GTree *tree, - | ^~~~~~~~~~~~~~~ -gam.c: In function 'GAM_report': -gam.c:589:9: warning: 'g_tree_traverse' is deprecated [-Wdeprecated-declarations] - 589 | g_tree_traverse(gam->bestn_tree, GAM_bestn_tree_report_traverse, - | ^~~~~~~~~~~~~~~ -/usr/include/glib-2.0/glib/gtree.h:148:10: note: declared here - 148 | void g_tree_traverse (GTree *tree, - | ^~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 bsam.test bsam.test.o bsam.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/threadref.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/sequence/splice.o ../../src/struct/dejavu.o ../../src/struct/pqueue.o ../../src/struct/sparsecache.o ../../src/struct/recyclebin.o ../../src/struct/matrix.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 gam.test gam.test.o gam.o ../../src/comparison/hspset.o ../../src/comparison/comparison.o ../../src/comparison/wordhood.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 analysis.test analysis.test.o analysis.o gam.o bsam.o ../../src/comparison/hspset.o ../../src/comparison/wordhood.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/general/compoundfile.o ../../src/general/socket.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/viterbi.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/scheduler.o ../../src/sdp/straceback.o ../../src/sdp/lookahead.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -lglib-2.0 @@ -1397,1432 +1440,1432 @@ Making all in program make[3]: Entering directory '/build/exonerate-2.4.0/src/program' ../../src/model/bootstrapper --compiled no -** Message: 14:27:52.523: Starting building bootstrapping components -** Message: 14:27:52.523: Processing model [u] -** Message: 14:27:52.524: Bootstrapper processing model [ungapped:dna2dna] -** Message: 14:27:52.524: Process optimal [optimal:ungapped:dna2dna] +** Message: 23:19:50.709: Starting building bootstrapping components +** Message: 23:19:50.709: Processing model [u] +** Message: 23:19:50.710: Bootstrapper processing model [ungapped:dna2dna] +** Message: 23:19:50.710: Process optimal [optimal:ungapped:dna2dna] -** (process:5079): WARNING **: 14:27:52.524: Creating codegen directory [/build/exonerate-2.4.0/codegen] +** (process:57867): WARNING **: 23:19:50.710: Creating codegen directory [/build/exonerate-2.4.0/codegen] -** (process:5079): WARNING **: 14:27:52.524: Creating codegen directory [/build/exonerate-2.4.0/codegen] +** (process:57867): WARNING **: 23:19:50.710: Creating codegen directory [/build/exonerate-2.4.0/codegen] -** (process:5079): WARNING **: 14:27:52.524: Creating codegen directory [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu] +** (process:57867): WARNING **: 23:19:50.710: Creating codegen directory [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu] -** (process:5079): WARNING **: 14:27:52.524: Creating codegen directory [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu] -** Message: 14:27:52.525: Compiling codegen: +** (process:57867): WARNING **: 23:19:50.710: Creating codegen directory [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu] +** Message: 23:19:50.710: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.c -** Message: 14:27:52.857: Compiling codegen: +** Message: 23:19:50.857: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.c -** Message: 14:27:53.255: Compiling codegen: +** Message: 23:19:51.024: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.c -** Message: 14:27:53.716: Compiling codegen: +** Message: 23:19:51.201: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.c -** Message: 14:27:54.305: Compiling codegen: +** Message: 23:19:51.497: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 14:27:54.920: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] -** Message: 14:27:54.920: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] to archive +** Message: 23:19:51.756: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o] +** Message: 23:19:51.756: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_score.o -** Message: 14:27:54.932: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] -** Message: 14:27:54.932: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] -** Message: 14:27:54.932: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] to archive +** Message: 23:19:51.758: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_score] +** Message: 23:19:51.758: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o] +** Message: 23:19:51.758: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path.o -** Message: 14:27:54.944: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] -** Message: 14:27:54.944: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] -** Message: 14:27:54.944: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] to archive +** Message: 23:19:51.761: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path] +** Message: 23:19:51.761: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o] +** Message: 23:19:51.761: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_region.o -** Message: 14:27:54.963: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] -** Message: 14:27:54.963: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] -** Message: 14:27:54.963: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 23:19:51.763: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_region] +** Message: 23:19:51.763: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o] +** Message: 23:19:51.763: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint.o -** Message: 14:27:54.967: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] -** Message: 14:27:54.967: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 14:27:54.967: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] to archive +** Message: 23:19:51.766: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_checkpoint] +** Message: 23:19:51.766: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 23:19:51.766: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 14:27:54.974: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] -** Message: 14:27:54.974: Bootstrapper processing model [ungapped:protein2protein] -** Message: 14:27:54.974: Process optimal [optimal:ungapped:protein2protein] -** Message: 14:27:54.974: Compiling codegen: +** Message: 23:19:51.768: Adding function [optimal_58_ungapped_58_dna2dna_32_find_32_path_32_continuation] +** Message: 23:19:51.768: Bootstrapper processing model [ungapped:protein2protein] +** Message: 23:19:51.768: Process optimal [optimal:ungapped:protein2protein] +** Message: 23:19:51.769: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.c -** Message: 14:27:55.336: Compiling codegen: +** Message: 23:19:51.916: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.c -** Message: 14:27:55.700: Compiling codegen: +** Message: 23:19:52.081: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.c -** Message: 14:27:56.080: Compiling codegen: +** Message: 23:19:52.253: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.c -** Message: 14:27:56.665: Compiling codegen: +** Message: 23:19:52.567: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.c -** Message: 14:27:57.224: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] -** Message: 14:27:57.224: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] to archive +** Message: 23:19:52.812: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o] +** Message: 23:19:52.812: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_score.o -** Message: 14:27:57.236: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] -** Message: 14:27:57.236: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] -** Message: 14:27:57.236: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] to archive +** Message: 23:19:52.815: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_score] +** Message: 23:19:52.815: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o] +** Message: 23:19:52.815: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path.o -** Message: 14:27:57.252: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] -** Message: 14:27:57.252: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] -** Message: 14:27:57.252: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] to archive +** Message: 23:19:52.818: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path] +** Message: 23:19:52.818: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o] +** Message: 23:19:52.818: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_region.o -** Message: 14:27:57.276: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] -** Message: 14:27:57.276: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] -** Message: 14:27:57.276: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] to archive +** Message: 23:19:52.820: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_region] +** Message: 23:19:52.820: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o] +** Message: 23:19:52.820: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint.o -** Message: 14:27:57.304: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] -** Message: 14:27:57.304: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] -** Message: 14:27:57.304: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] to archive +** Message: 23:19:52.823: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_checkpoint] +** Message: 23:19:52.823: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o] +** Message: 23:19:52.823: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation.o -** Message: 14:27:57.314: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] -** Message: 14:27:57.314: Bootstrapper processing model [ungapped:dna2protein] -** Message: 14:27:57.314: Process optimal [optimal:ungapped:dna2protein] -** Message: 14:27:57.315: Compiling codegen: +** Message: 23:19:52.826: Adding function [optimal_58_ungapped_58_protein2protein_32_find_32_path_32_continuation] +** Message: 23:19:52.826: Bootstrapper processing model [ungapped:dna2protein] +** Message: 23:19:52.826: Process optimal [optimal:ungapped:dna2protein] +** Message: 23:19:52.827: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.c -** Message: 14:27:57.724: Compiling codegen: +** Message: 23:19:53.005: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.c -** Message: 14:27:58.292: Compiling codegen: +** Message: 23:19:53.229: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.c -** Message: 14:27:58.864: Compiling codegen: +** Message: 23:19:53.471: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.c -** Message: 14:27:59.627: Compiling codegen: +** Message: 23:19:53.849: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.c -** Message: 14:28:00.417: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] -** Message: 14:28:00.417: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] to archive +** Message: 23:19:54.163: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o] +** Message: 23:19:54.163: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_score.o -** Message: 14:28:00.440: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] -** Message: 14:28:00.440: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] -** Message: 14:28:00.440: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] to archive +** Message: 23:19:54.166: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_score] +** Message: 23:19:54.166: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o] +** Message: 23:19:54.166: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path.o -** Message: 14:28:00.460: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] -** Message: 14:28:00.460: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] -** Message: 14:28:00.460: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] to archive +** Message: 23:19:54.233: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path] +** Message: 23:19:54.233: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o] +** Message: 23:19:54.233: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_region.o -** Message: 14:28:00.474: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] -** Message: 14:28:00.474: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] -** Message: 14:28:00.474: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] to archive +** Message: 23:19:54.236: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_region] +** Message: 23:19:54.236: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o] +** Message: 23:19:54.236: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint.o -** Message: 14:28:00.484: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] -** Message: 14:28:00.484: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] -** Message: 14:28:00.484: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] to archive +** Message: 23:19:54.239: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_checkpoint] +** Message: 23:19:54.239: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o] +** Message: 23:19:54.239: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation.o -** Message: 14:28:00.498: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] -** Message: 14:28:00.499: Bootstrapper processing model [ungapped:protein2dna] -** Message: 14:28:00.499: Process optimal [optimal:ungapped:protein2dna] -** Message: 14:28:00.499: Compiling codegen: +** Message: 23:19:54.243: Adding function [optimal_58_ungapped_58_dna2protein_32_find_32_path_32_continuation] +** Message: 23:19:54.243: Bootstrapper processing model [ungapped:protein2dna] +** Message: 23:19:54.243: Process optimal [optimal:ungapped:protein2dna] +** Message: 23:19:54.243: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.c -** Message: 14:28:00.913: Compiling codegen: +** Message: 23:19:54.416: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.c -** Message: 14:28:01.409: Compiling codegen: +** Message: 23:19:54.620: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.c -** Message: 14:28:01.908: Compiling codegen: +** Message: 23:19:54.844: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.c -** Message: 14:28:02.781: Compiling codegen: +** Message: 23:19:55.208: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.c -** Message: 14:28:03.501: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] -** Message: 14:28:03.501: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] to archive +** Message: 23:19:55.518: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o] +** Message: 23:19:55.518: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_score.o -** Message: 14:28:03.507: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] -** Message: 14:28:03.507: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] -** Message: 14:28:03.507: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] to archive +** Message: 23:19:55.522: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_score] +** Message: 23:19:55.522: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o] +** Message: 23:19:55.522: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path.o -** Message: 14:28:03.513: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] -** Message: 14:28:03.513: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] -** Message: 14:28:03.513: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] to archive +** Message: 23:19:55.525: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path] +** Message: 23:19:55.525: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o] +** Message: 23:19:55.525: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_region.o -** Message: 14:28:03.520: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] -** Message: 14:28:03.520: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] -** Message: 14:28:03.520: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] to archive +** Message: 23:19:55.529: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_region] +** Message: 23:19:55.529: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o] +** Message: 23:19:55.529: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint.o -** Message: 14:28:03.528: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] -** Message: 14:28:03.528: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] -** Message: 14:28:03.528: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] to archive +** Message: 23:19:55.532: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_checkpoint] +** Message: 23:19:55.532: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o] +** Message: 23:19:55.532: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation.o -** Message: 14:28:03.535: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] -** Message: 14:28:03.535: Processing model [u:t] -** Message: 14:28:03.535: Bootstrapper processing model [ungapped:codon] -** Message: 14:28:03.535: Process optimal [optimal:ungapped:codon] -** Message: 14:28:03.536: Compiling codegen: +** Message: 23:19:55.536: Adding function [optimal_58_ungapped_58_protein2dna_32_find_32_path_32_continuation] +** Message: 23:19:55.536: Processing model [u:t] +** Message: 23:19:55.536: Bootstrapper processing model [ungapped:codon] +** Message: 23:19:55.536: Process optimal [optimal:ungapped:codon] +** Message: 23:19:55.537: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.c -** Message: 14:28:04.098: Compiling codegen: +** Message: 23:19:55.789: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.c -** Message: 14:28:04.933: Compiling codegen: +** Message: 23:19:56.099: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.c -** Message: 14:28:05.881: Compiling codegen: +** Message: 23:19:56.465: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.c -** Message: 14:28:07.077: Compiling codegen: +** Message: 23:19:56.994: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.c -** Message: 14:28:08.181: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] -** Message: 14:28:08.181: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] to archive +** Message: 23:19:57.476: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o] +** Message: 23:19:57.476: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_score.o -** Message: 14:28:08.190: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] -** Message: 14:28:08.190: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] -** Message: 14:28:08.190: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] to archive +** Message: 23:19:57.480: Adding function [optimal_58_ungapped_58_codon_32_find_32_score] +** Message: 23:19:57.480: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o] +** Message: 23:19:57.480: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path.o -** Message: 14:28:08.208: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] -** Message: 14:28:08.208: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] -** Message: 14:28:08.208: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] to archive +** Message: 23:19:57.484: Adding function [optimal_58_ungapped_58_codon_32_find_32_path] +** Message: 23:19:57.484: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o] +** Message: 23:19:57.484: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_region.o -** Message: 14:28:08.217: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] -** Message: 14:28:08.217: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] -** Message: 14:28:08.217: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] to archive +** Message: 23:19:57.488: Adding function [optimal_58_ungapped_58_codon_32_find_32_region] +** Message: 23:19:57.488: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o] +** Message: 23:19:57.488: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_checkpoint.o -** Message: 14:28:08.232: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] -** Message: 14:28:08.232: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] -** Message: 14:28:08.232: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] to archive +** Message: 23:19:57.492: Adding function [optimal_58_ungapped_58_codon_32_find_32_checkpoint] +** Message: 23:19:57.492: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o] +** Message: 23:19:57.492: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_ungapped_58_codon_32_find_32_path_32_continuation.o -** Message: 14:28:08.250: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] -** Message: 14:28:08.250: Processing model [a:g] -** Message: 14:28:08.250: Bootstrapper processing model [affine:global:dna2dna] -** Message: 14:28:08.250: Process optimal [optimal:affine:global:dna2dna] -** Message: 14:28:08.251: Compiling codegen: +** Message: 23:19:57.496: Adding function [optimal_58_ungapped_58_codon_32_find_32_path_32_continuation] +** Message: 23:19:57.496: Processing model [a:g] +** Message: 23:19:57.496: Bootstrapper processing model [affine:global:dna2dna] +** Message: 23:19:57.496: Process optimal [optimal:affine:global:dna2dna] +** Message: 23:19:57.497: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.c -** Message: 14:28:09.048: Compiling codegen: +** Message: 23:19:57.852: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.c -** Message: 14:28:10.214: Compiling codegen: +** Message: 23:19:58.357: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.c -** Message: 14:28:11.470: Compiling codegen: +** Message: 23:19:58.870: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 14:28:12.807: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] -** Message: 14:28:12.807: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] to archive +** Message: 23:19:59.451: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o] +** Message: 23:19:59.451: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_score.o -** Message: 14:28:12.820: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] -** Message: 14:28:12.820: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] -** Message: 14:28:12.820: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] to archive +** Message: 23:19:59.455: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_score] +** Message: 23:19:59.455: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o] +** Message: 23:19:59.455: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path.o -** Message: 14:28:12.830: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] -** Message: 14:28:12.831: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] -** Message: 14:28:12.831: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 23:19:59.460: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path] +** Message: 23:19:59.460: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o] +** Message: 23:19:59.460: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint.o -** Message: 14:28:12.845: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] -** Message: 14:28:12.845: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 14:28:12.845: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] to archive +** Message: 23:19:59.465: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_checkpoint] +** Message: 23:19:59.465: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 23:19:59.465: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 14:28:12.856: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] -** Message: 14:28:12.857: Bootstrapper processing model [affine:global:protein2protein] -** Message: 14:28:12.857: Process optimal [optimal:affine:global:protein2protein] -** Message: 14:28:12.857: Compiling codegen: +** Message: 23:19:59.469: Adding function [optimal_58_affine_58_global_58_dna2dna_32_find_32_path_32_continuation] +** Message: 23:19:59.469: Bootstrapper processing model [affine:global:protein2protein] +** Message: 23:19:59.469: Process optimal [optimal:affine:global:protein2protein] +** Message: 23:19:59.470: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.c -** Message: 14:28:13.464: Compiling codegen: +** Message: 23:19:59.821: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.c -** Message: 14:28:14.641: Compiling codegen: +** Message: 23:20:00.325: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.c -** Message: 14:28:15.802: Compiling codegen: +** Message: 23:20:00.825: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.c -** Message: 14:28:16.768: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] -** Message: 14:28:16.769: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] to archive +** Message: 23:20:01.404: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o] +** Message: 23:20:01.404: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_score.o -** Message: 14:28:16.779: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] -** Message: 14:28:16.779: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] -** Message: 14:28:16.779: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] to archive +** Message: 23:20:01.409: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_score] +** Message: 23:20:01.409: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o] +** Message: 23:20:01.409: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path.o -** Message: 14:28:16.789: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] -** Message: 14:28:16.789: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] -** Message: 14:28:16.789: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] to archive +** Message: 23:20:01.414: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path] +** Message: 23:20:01.414: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o] +** Message: 23:20:01.414: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint.o -** Message: 14:28:16.800: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] -** Message: 14:28:16.800: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] -** Message: 14:28:16.800: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] to archive +** Message: 23:20:01.419: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_checkpoint] +** Message: 23:20:01.419: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o] +** Message: 23:20:01.419: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation.o -** Message: 14:28:16.809: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] -** Message: 14:28:16.809: Processing model [a:b] -** Message: 14:28:16.809: Bootstrapper processing model [affine:bestfit:dna2dna] -** Message: 14:28:16.809: Process optimal [optimal:affine:bestfit:dna2dna] -** Message: 14:28:16.811: Compiling codegen: +** Message: 23:20:01.423: Adding function [optimal_58_affine_58_global_58_protein2protein_32_find_32_path_32_continuation] +** Message: 23:20:01.424: Processing model [a:b] +** Message: 23:20:01.424: Bootstrapper processing model [affine:bestfit:dna2dna] +** Message: 23:20:01.424: Process optimal [optimal:affine:bestfit:dna2dna] +** Message: 23:20:01.425: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.c -** Message: 14:28:17.626: Compiling codegen: +** Message: 23:20:01.894: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.c -** Message: 14:28:19.230: Compiling codegen: +** Message: 23:20:02.611: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.c -** Message: 14:28:20.700: Compiling codegen: +** Message: 23:20:03.242: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.c -** Message: 14:28:21.857: Compiling codegen: +** Message: 23:20:03.754: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 14:28:22.886: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] -** Message: 14:28:22.886: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] to archive +** Message: 23:20:04.326: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o] +** Message: 23:20:04.326: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score.o -** Message: 14:28:22.898: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] -** Message: 14:28:22.898: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] -** Message: 14:28:22.898: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] to archive +** Message: 23:20:04.332: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_score] +** Message: 23:20:04.332: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o] +** Message: 23:20:04.332: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path.o -** Message: 14:28:22.911: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] -** Message: 14:28:22.911: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] -** Message: 14:28:22.911: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] to archive +** Message: 23:20:04.337: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path] +** Message: 23:20:04.337: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o] +** Message: 23:20:04.337: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region.o -** Message: 14:28:22.923: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] -** Message: 14:28:22.923: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] -** Message: 14:28:22.923: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 23:20:04.342: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_region] +** Message: 23:20:04.342: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o] +** Message: 23:20:04.342: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint.o -** Message: 14:28:22.939: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] -** Message: 14:28:22.939: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 14:28:22.939: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] to archive +** Message: 23:20:04.347: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_checkpoint] +** Message: 23:20:04.347: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 23:20:04.347: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 14:28:22.953: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] -** Message: 14:28:22.953: Bootstrapper processing model [affine:bestfit:protein2protein] -** Message: 14:28:22.953: Process optimal [optimal:affine:bestfit:protein2protein] -** Message: 14:28:22.955: Compiling codegen: +** Message: 23:20:04.352: Adding function [optimal_58_affine_58_bestfit_58_dna2dna_32_find_32_path_32_continuation] +** Message: 23:20:04.352: Bootstrapper processing model [affine:bestfit:protein2protein] +** Message: 23:20:04.352: Process optimal [optimal:affine:bestfit:protein2protein] +** Message: 23:20:04.353: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.c -** Message: 14:28:23.721: Compiling codegen: +** Message: 23:20:04.811: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.c -** Message: 14:28:25.292: Compiling codegen: +** Message: 23:20:05.501: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.c -** Message: 14:28:26.765: Compiling codegen: +** Message: 23:20:06.139: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.c -** Message: 14:28:27.967: Compiling codegen: +** Message: 23:20:06.650: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.c -** Message: 14:28:29.263: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] -** Message: 14:28:29.263: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] to archive +** Message: 23:20:07.219: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o] +** Message: 23:20:07.219: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score.o -** Message: 14:28:29.278: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] -** Message: 14:28:29.278: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] -** Message: 14:28:29.278: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] to archive +** Message: 23:20:07.225: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_score] +** Message: 23:20:07.225: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o] +** Message: 23:20:07.225: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path.o -** Message: 14:28:29.293: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] -** Message: 14:28:29.293: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] -** Message: 14:28:29.293: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] to archive +** Message: 23:20:07.231: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path] +** Message: 23:20:07.231: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o] +** Message: 23:20:07.231: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region.o -** Message: 14:28:29.324: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] -** Message: 14:28:29.324: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] -** Message: 14:28:29.324: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] to archive +** Message: 23:20:07.237: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_region] +** Message: 23:20:07.237: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o] +** Message: 23:20:07.237: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint.o -** Message: 14:28:29.338: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] -** Message: 14:28:29.338: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] -** Message: 14:28:29.338: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] to archive +** Message: 23:20:07.243: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_checkpoint] +** Message: 23:20:07.243: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o] +** Message: 23:20:07.243: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation.o -** Message: 14:28:29.354: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] -** Message: 14:28:29.354: Processing model [a:l] -** Message: 14:28:29.354: Bootstrapper processing model [affine:local:dna2dna] -** Message: 14:28:29.354: Process optimal [optimal:affine:local:dna2dna] -** Message: 14:28:29.355: Compiling codegen: +** Message: 23:20:07.248: Adding function [optimal_58_affine_58_bestfit_58_protein2protein_32_find_32_path_32_continuation] +** Message: 23:20:07.249: Processing model [a:l] +** Message: 23:20:07.249: Bootstrapper processing model [affine:local:dna2dna] +** Message: 23:20:07.249: Process optimal [optimal:affine:local:dna2dna] +** Message: 23:20:07.249: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.c -** Message: 14:28:29.829: Compiling codegen: +** Message: 23:20:07.456: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.c -** Message: 14:28:30.439: Compiling codegen: +** Message: 23:20:07.736: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.c -** Message: 14:28:31.097: Compiling codegen: +** Message: 23:20:08.016: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c -** Message: 14:28:32.293: Compiling codegen: +** Message: 23:20:08.558: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 14:28:33.604: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] -** Message: 14:28:33.604: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive +** Message: 23:20:09.128: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o] +** Message: 23:20:09.128: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_score.o -** Message: 14:28:33.652: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] -** Message: 14:28:33.652: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] -** Message: 14:28:33.652: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive +** Message: 23:20:09.135: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_score] +** Message: 23:20:09.135: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o] +** Message: 23:20:09.135: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path.o -** Message: 14:28:33.680: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] -** Message: 14:28:33.680: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] -** Message: 14:28:33.680: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive +** Message: 23:20:09.142: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path] +** Message: 23:20:09.142: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o] +** Message: 23:20:09.142: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_region.o -** Message: 14:28:33.703: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] -** Message: 14:28:33.703: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] -** Message: 14:28:33.704: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 23:20:09.148: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_region] +** Message: 23:20:09.148: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] +** Message: 23:20:09.148: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -** Message: 14:28:33.723: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] -** Message: 14:28:33.723: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 14:28:33.723: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] to archive +** Message: 23:20:09.154: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] +** Message: 23:20:09.154: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 23:20:09.154: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 14:28:33.742: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] -** Message: 14:28:33.746: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] -** Message: 14:28:33.747: Compiling codegen: +** Message: 23:20:09.161: Adding function [optimal_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] +** Message: 23:20:09.162: Process optimal [Terminal [Segment("START"->"match"):[affine:local:dna2dna]]] +** Message: 23:20:09.163: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:34.697: Compiling codegen: +** Message: 23:20:09.608: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:36.140: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:36.140: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:10.201: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:10.202: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:36.184: 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: 14:28:36.184: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:36.184: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:10.209: 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: 23:20:10.209: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:10.209: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:36.220: 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: 14:28:36.220: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] -** Message: 14:28:36.221: Compiling codegen: +** Message: 23:20:10.216: 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: 23:20:10.216: Process optimal [Terminal [Segment("match"->"END"):[affine:local:dna2dna]]] +** Message: 23:20:10.216: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:36.974: Compiling codegen: +** Message: 23:20:10.638: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:38.088: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:38.088: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:11.110: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:11.110: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:38.110: 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: 14:28:38.110: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:38.110: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:11.117: 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: 23:20:11.117: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:11.117: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:38.133: 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: 14:28:38.133: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] -** Message: 14:28:38.136: Compiling codegen: +** Message: 23:20:11.124: 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: 23:20:11.124: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:dna2dna]]] +** Message: 23:20:11.126: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:40.191: Compiling codegen: +** Message: 23:20:12.026: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:43.363: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:43.363: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:13.448: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:13.448: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:43.384: 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: 14:28:43.384: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:43.384: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:13.456: 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: 23:20:13.456: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:13.456: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:43.404: 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: 14:28:43.405: Compiling codegen: +** Message: 23:20:13.464: 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: 23:20:13.465: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.c -** Message: 14:28:43.894: Compiling codegen: +** Message: 23:20:13.687: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.c -** Message: 14:28:44.375: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] -** Message: 14:28:44.375: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] to archive +** Message: 23:20:13.998: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o] +** Message: 23:20:13.998: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded.o -** Message: 14:28:44.395: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] -** Message: 14:28:44.395: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] -** Message: 14:28:44.395: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] to archive +** Message: 23:20:14.006: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_reverse_58_traceback_58_seeded] +** Message: 23:20:14.006: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o] +** Message: 23:20:14.006: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded.o -** Message: 14:28:44.415: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] -** Message: 14:28:44.415: Bootstrapper processing model [affine:local:protein2protein] -** Message: 14:28:44.415: Process optimal [optimal:affine:local:protein2protein] -** Message: 14:28:44.416: Compiling codegen: +** Message: 23:20:14.014: Adding function [Scheduler_Cell_process_affine_58_local_58_dna2dna_58_forward_58_traceback_58_seeded] +** Message: 23:20:14.014: Bootstrapper processing model [affine:local:protein2protein] +** Message: 23:20:14.014: Process optimal [optimal:affine:local:protein2protein] +** Message: 23:20:14.015: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.c -** Message: 14:28:44.883: Compiling codegen: +** Message: 23:20:14.219: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.c -** Message: 14:28:45.565: Compiling codegen: +** Message: 23:20:14.488: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.c -** Message: 14:28:46.172: Compiling codegen: +** Message: 23:20:14.839: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c -** Message: 14:28:47.288: Compiling codegen: +** Message: 23:20:15.345: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c -** Message: 14:28:48.546: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] -** Message: 14:28:48.546: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive +** Message: 23:20:15.921: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o] +** Message: 23:20:15.921: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_score.o -** Message: 14:28:48.567: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] -** Message: 14:28:48.567: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] -** Message: 14:28:48.567: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive +** Message: 23:20:15.929: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_score] +** Message: 23:20:15.929: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o] +** Message: 23:20:15.929: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path.o -** Message: 14:28:48.583: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] -** Message: 14:28:48.583: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] -** Message: 14:28:48.583: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive +** Message: 23:20:15.936: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path] +** Message: 23:20:15.936: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o] +** Message: 23:20:15.936: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_region.o -** Message: 14:28:48.605: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] -** Message: 14:28:48.605: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] -** Message: 14:28:48.605: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive +** Message: 23:20:15.945: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_region] +** Message: 23:20:15.945: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] +** Message: 23:20:15.945: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -** Message: 14:28:48.621: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] -** Message: 14:28:48.621: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] -** Message: 14:28:48.621: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] to archive +** Message: 23:20:15.952: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] +** Message: 23:20:15.952: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] +** Message: 23:20:15.952: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -** Message: 14:28:48.642: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] -** Message: 14:28:48.644: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] -** Message: 14:28:48.646: Compiling codegen: +** Message: 23:20:15.960: Adding function [optimal_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] +** Message: 23:20:15.963: Process optimal [Terminal [Segment("START"->"match"):[affine:local:protein2protein]]] +** Message: 23:20:15.964: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:49.335: Compiling codegen: +** Message: 23:20:16.358: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:50.364: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:50.364: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:16.948: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:16.948: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:50.412: 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: 14:28:50.412: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:50.412: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:16.957: 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: 23:20:16.957: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:16.957: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:50.452: 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: 14:28:50.452: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] -** Message: 14:28:50.453: Compiling codegen: +** Message: 23:20:16.965: 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: 23:20:16.965: Process optimal [Terminal [Segment("match"->"END"):[affine:local:protein2protein]]] +** Message: 23:20:16.966: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:51.193: Compiling codegen: +** Message: 23:20:17.347: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:52.304: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:52.304: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:17.814: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:17.814: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:52.332: 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: 14:28:52.332: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:52.332: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:17.823: 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: 23:20:17.823: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:17.823: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:52.356: 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: 14:28:52.356: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] -** Message: 14:28:52.358: Compiling codegen: +** Message: 23:20:17.831: 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: 23:20:17.831: Process optimal [HeuristicJoin:[Segment("match"->"match"):[affine:local:protein2protein]]] +** Message: 23:20:17.833: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:54.419: Compiling codegen: +** Message: 23:20:18.685: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:57.564: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:57.564: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:20.093: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:20.093: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:57.616: 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: 14:28:57.616: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:28:57.616: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:20.109: 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: 23:20:20.109: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:20.109: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:28:57.656: 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: 14:28:57.656: Compiling codegen: +** Message: 23:20:20.124: 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: 23:20:20.125: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.c -** Message: 14:28:58.177: Compiling codegen: +** Message: 23:20:20.505: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.c -** Message: 14:28:58.663: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] -** Message: 14:28:58.663: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] to archive +** Message: 23:20:20.928: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o] +** Message: 23:20:20.928: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded.o -** Message: 14:28:58.685: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] -** Message: 14:28:58.685: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] -** Message: 14:28:58.685: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] to archive +** Message: 23:20:20.944: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_reverse_58_traceback_58_seeded] +** Message: 23:20:20.944: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o] +** Message: 23:20:20.944: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded.o -** Message: 14:28:58.707: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] -** Message: 14:28:58.707: Processing model [a:o] -** Message: 14:28:58.708: Bootstrapper processing model [affine:overlap:dna2dna] -** Message: 14:28:58.708: Process optimal [optimal:affine:overlap:dna2dna] -** Message: 14:28:58.709: Compiling codegen: +** Message: 23:20:20.962: Adding function [Scheduler_Cell_process_affine_58_local_58_protein2protein_58_forward_58_traceback_58_seeded] +** Message: 23:20:20.962: Processing model [a:o] +** Message: 23:20:20.962: Bootstrapper processing model [affine:overlap:dna2dna] +** Message: 23:20:20.963: Process optimal [optimal:affine:overlap:dna2dna] +** Message: 23:20:20.964: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.c -** Message: 14:28:59.567: Compiling codegen: +** Message: 23:20:21.650: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.c -** Message: 14:29:00.871: Compiling codegen: +** Message: 23:20:22.724: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.c -** Message: 14:29:01.999: Compiling codegen: +** Message: 23:20:23.899: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.c -** Message: 14:29:02.863: Compiling codegen: +** Message: 23:20:24.738: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 14:29:03.892: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] -** Message: 14:29:03.892: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] to archive +** Message: 23:20:25.442: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o] +** Message: 23:20:25.442: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score.o -** Message: 14:29:03.917: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] -** Message: 14:29:03.917: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] -** Message: 14:29:03.918: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] to archive +** Message: 23:20:25.456: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_score] +** Message: 23:20:25.456: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o] +** Message: 23:20:25.456: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path.o -** Message: 14:29:03.938: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] -** Message: 14:29:03.938: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] -** Message: 14:29:03.938: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] to archive +** Message: 23:20:25.469: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path] +** Message: 23:20:25.469: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o] +** Message: 23:20:25.469: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region.o -** Message: 14:29:03.965: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] -** Message: 14:29:03.965: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] -** Message: 14:29:03.965: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 23:20:25.481: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_region] +** Message: 23:20:25.481: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o] +** Message: 23:20:25.481: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint.o -** Message: 14:29:03.989: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] -** Message: 14:29:03.989: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 14:29:03.989: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] to archive +** Message: 23:20:25.494: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_checkpoint] +** Message: 23:20:25.494: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 23:20:25.494: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 14:29:04.011: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] -** Message: 14:29:04.011: Processing model [e2g] -** Message: 14:29:04.012: Bootstrapper processing model [est2genome] -** Message: 14:29:04.012: Process optimal [optimal:est2genome] -** Message: 14:29:04.014: Compiling codegen: +** Message: 23:20:25.507: Adding function [optimal_58_affine_58_overlap_58_dna2dna_32_find_32_path_32_continuation] +** Message: 23:20:25.507: Processing model [e2g] +** Message: 23:20:25.508: Bootstrapper processing model [est2genome] +** Message: 23:20:25.508: Process optimal [optimal:est2genome] +** Message: 23:20:25.509: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.c -** Message: 14:29:05.367: Compiling codegen: +** Message: 23:20:26.379: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.c -** Message: 14:29:07.399: Compiling codegen: +** Message: 23:20:27.605: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.c -** Message: 14:29:09.303: Compiling codegen: +** Message: 23:20:28.765: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.c -** Message: 14:29:14.240: Compiling codegen: +** Message: 23:20:32.146: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.c -** Message: 14:29:20.737: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] -** Message: 14:29:20.737: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] to archive +** Message: 23:20:36.092: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] +** Message: 23:20:36.092: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_score.o -** Message: 14:29:20.758: Adding function [optimal_58_est2genome_32_find_32_score] -** Message: 14:29:20.758: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] -** Message: 14:29:20.758: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] to archive +** Message: 23:20:36.102: Adding function [optimal_58_est2genome_32_find_32_score] +** Message: 23:20:36.102: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] +** Message: 23:20:36.102: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path.o -** Message: 14:29:20.780: Adding function [optimal_58_est2genome_32_find_32_path] -** Message: 14:29:20.780: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] -** Message: 14:29:20.780: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] to archive +** Message: 23:20:36.113: Adding function [optimal_58_est2genome_32_find_32_path] +** Message: 23:20:36.113: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] +** Message: 23:20:36.113: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_region.o -** Message: 14:29:20.802: Adding function [optimal_58_est2genome_32_find_32_region] -** Message: 14:29:20.802: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] -** Message: 14:29:20.802: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] to archive +** Message: 23:20:36.122: Adding function [optimal_58_est2genome_32_find_32_region] +** Message: 23:20:36.122: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] +** Message: 23:20:36.122: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_checkpoint.o -** Message: 14:29:20.825: Adding function [optimal_58_est2genome_32_find_32_checkpoint] -** Message: 14:29:20.825: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] -** Message: 14:29:20.825: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] to archive +** Message: 23:20:36.132: Adding function [optimal_58_est2genome_32_find_32_checkpoint] +** Message: 23:20:36.132: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o] +** Message: 23:20:36.132: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_est2genome_32_find_32_path_32_continuation.o -** Message: 14:29:20.849: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] -** Message: 14:29:20.859: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] -** Message: 14:29:20.862: Compiling codegen: +** Message: 23:20:36.143: Adding function [optimal_58_est2genome_32_find_32_path_32_continuation] +** Message: 23:20:36.150: Process optimal [Terminal [Segment("START"->"match reverse"):[est2genome]]] +** Message: 23:20:36.151: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:22.747: Compiling codegen: +** Message: 23:20:37.281: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:26.092: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:26.092: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:39.114: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:39.114: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:26.121: 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: 14:29:26.121: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:26.121: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:39.127: 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: 23:20:39.127: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:39.127: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:26.150: 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: 14:29:26.150: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] -** Message: 14:29:26.152: Compiling codegen: +** Message: 23:20:39.140: 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: 23:20:39.140: Process optimal [Terminal [Segment("match reverse"->"END"):[est2genome]]] +** Message: 23:20:39.141: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:27.430: Compiling codegen: +** Message: 23:20:39.843: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:29.976: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:29.976: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:40.844: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:40.844: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:30.048: 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: 14:29:30.048: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:30.048: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:40.857: 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: 23:20:40.857: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:40.857: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:30.104: 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: 14:29:30.104: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] -** Message: 14:29:30.107: Compiling codegen: +** Message: 23:20:40.869: 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: 23:20:40.869: Process optimal [Terminal [Segment("START"->"match forward"):[est2genome]]] +** Message: 23:20:40.871: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:32.652: Compiling codegen: +** Message: 23:20:42.038: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:36.794: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:36.794: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:43.903: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:43.903: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:36.822: 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: 14:29:36.823: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:36.823: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:43.916: 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: 23:20:43.916: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:43.916: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:36.850: 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: 14:29:36.850: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] -** Message: 14:29:36.853: Compiling codegen: +** Message: 23:20:43.930: 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: 23:20:43.930: Process optimal [Terminal [Segment("match forward"->"END"):[est2genome]]] +** Message: 23:20:43.931: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:38.436: Compiling codegen: +** Message: 23:20:44.635: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:40.296: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:40.296: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:45.655: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:45.655: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:40.330: 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: 14:29:40.330: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:40.330: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:45.668: 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: 23:20:45.668: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:45.668: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:40.367: 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: 14:29:40.367: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] -** Message: 14:29:40.372: Compiling codegen: +** Message: 23:20:45.681: 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: 23:20:45.681: Process optimal [HeuristicJoin:[Segment("match reverse"->"match reverse"):[est2genome]]] +** Message: 23:20:45.683: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:45.437: Compiling codegen: +** Message: 23:20:47.982: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:54.420: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:54.420: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:51.980: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:51.980: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:54.456: 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: 14:29:54.456: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:54.456: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:51.994: 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: 23:20:51.994: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:51.994: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:54.494: 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: 14:29:54.494: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] -** Message: 14:29:54.497: Compiling codegen: +** Message: 23:20:52.008: 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: 23:20:52.008: Process optimal [Src span [Segment("match reverse"->"intron reverse"):[est2genome]]] +** Message: 23:20:52.009: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:56.101: Compiling codegen: +** Message: 23:20:52.754: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:58.488: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:58.489: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:53.839: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:53.839: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:58.536: 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: 14:29:58.536: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:29:58.536: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:53.852: 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: 23:20:53.852: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:53.852: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:29:58.575: 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: 14:29:58.575: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] -** Message: 14:29:58.579: Compiling codegen: +** Message: 23:20:53.866: 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: 23:20:53.866: Process optimal [Src span traceback [Segment("match reverse"->"intron reverse"):[est2genome]]] +** Message: 23:20:53.868: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:05.852: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:05.852: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:20:57.112: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:20:57.112: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:05.888: 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: 14:30:05.888: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] -** Message: 14:30:05.890: Compiling codegen: +** Message: 23:20:57.126: 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: 23:20:57.126: Process optimal [Dst span [Segment("intron reverse"->"match reverse"):[est2genome]]] +** Message: 23:20:57.127: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:08.715: Compiling codegen: +** Message: 23:20:58.353: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:13.257: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:13.257: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:00.430: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:00.431: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:13.303: 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: 14:30:13.303: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:13.303: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:00.445: 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: 23:21:00.445: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:00.445: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:13.345: 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: 14:30:13.345: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] -** Message: 14:30:13.351: Compiling codegen: +** Message: 23:21:00.459: 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: 23:21:00.459: Process optimal [HeuristicJoin:[Segment("match forward"->"match forward"):[est2genome]]] +** Message: 23:21:00.462: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:18.527: Compiling codegen: +** Message: 23:21:02.774: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:27.487: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:27.487: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:06.758: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:06.758: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:27.534: 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: 14:30:27.534: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:27.534: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:06.775: 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: 23:21:06.775: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:06.775: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:27.570: 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: 14:30:27.570: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] -** Message: 14:30:27.572: Compiling codegen: +** Message: 23:21:06.791: 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: 23:21:06.791: Process optimal [Src span [Segment("match forward"->"intron forward"):[est2genome]]] +** Message: 23:21:06.792: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:29.253: Compiling codegen: +** Message: 23:21:07.514: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:31.584: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:31.584: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:08.545: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:08.546: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:31.628: 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: 14:30:31.628: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:31.628: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:08.561: 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: 23:21:08.561: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:08.561: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:31.708: 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: 14:30:31.708: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] -** Message: 14:30:31.717: Compiling codegen: +** Message: 23:21:08.575: 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: 23:21:08.575: Process optimal [Src span traceback [Segment("match forward"->"intron forward"):[est2genome]]] +** Message: 23:21:08.578: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:37.996: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:37.996: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:11.791: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:11.791: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:38.118: 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: 14:30:38.118: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] -** Message: 14:30:38.121: Compiling codegen: +** Message: 23:21:11.806: 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: 23:21:11.807: Process optimal [Dst span [Segment("intron forward"->"match forward"):[est2genome]]] +** Message: 23:21:11.808: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:40.887: Compiling codegen: +** Message: 23:21:13.073: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:45.303: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:45.303: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:15.157: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:15.157: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:45.341: 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: 14:30:45.341: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:45.341: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:15.173: 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: 23:21:15.173: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:15.173: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:45.379: 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: 14:30:45.381: Compiling codegen: +** Message: 23:21:15.189: 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: 23:21:15.190: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.c -** Message: 14:30:46.349: Compiling codegen: +** Message: 23:21:15.599: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.c -** Message: 14:30:47.440: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] -** Message: 14:30:47.440: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] to archive +** Message: 23:21:16.043: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o] +** Message: 23:21:16.043: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary.o -** Message: 14:30:47.516: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] -** Message: 14:30:47.516: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] -** Message: 14:30:47.516: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] to archive +** Message: 23:21:16.059: Adding function [Scheduler_Cell_process_est2genome_58_reverse_58_notraceback_58_boundary] +** Message: 23:21:16.059: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o] +** Message: 23:21:16.059: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary.o -** Message: 14:30:47.556: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] -** Message: 14:30:47.556: Processing model [ner] -** Message: 14:30:47.556: Bootstrapper processing model [NER:affine:local:dna2dna] -** Message: 14:30:47.556: Process optimal [optimal:NER:affine:local:dna2dna] -** Message: 14:30:47.557: Compiling codegen: +** Message: 23:21:16.075: Adding function [Scheduler_Cell_process_est2genome_58_forward_58_traceback_58_boundary] +** Message: 23:21:16.075: Processing model [ner] +** Message: 23:21:16.075: Bootstrapper processing model [NER:affine:local:dna2dna] +** Message: 23:21:16.075: Process optimal [optimal:NER:affine:local:dna2dna] +** Message: 23:21:16.076: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.c -** Message: 14:30:48.041: Compiling codegen: +** Message: 23:21:16.318: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.c -** Message: 14:30:48.721: Compiling codegen: +** Message: 23:21:16.651: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.c -** Message: 14:30:49.487: Compiling codegen: +** Message: 23:21:16.995: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.c -** Message: 14:30:50.968: Compiling codegen: +** Message: 23:21:17.654: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.c -** Message: 14:30:52.656: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] -** Message: 14:30:52.657: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] to archive +** Message: 23:21:18.417: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o] +** Message: 23:21:18.417: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score.o -** Message: 14:30:52.708: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] -** Message: 14:30:52.708: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] -** Message: 14:30:52.708: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] to archive +** Message: 23:21:18.434: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_score] +** Message: 23:21:18.434: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o] +** Message: 23:21:18.434: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path.o -** Message: 14:30:52.750: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] -** Message: 14:30:52.750: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] -** Message: 14:30:52.750: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] to archive +** Message: 23:21:18.449: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path] +** Message: 23:21:18.450: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o] +** Message: 23:21:18.450: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region.o -** Message: 14:30:52.793: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] -** Message: 14:30:52.793: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] -** Message: 14:30:52.793: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] to archive +** Message: 23:21:18.465: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_region] +** Message: 23:21:18.465: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o] +** Message: 23:21:18.465: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint.o -** Message: 14:30:52.838: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] -** Message: 14:30:52.838: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] -** Message: 14:30:52.838: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:18.480: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_checkpoint] +** Message: 23:21:18.480: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o] +** Message: 23:21:18.480: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation.o -** Message: 14:30:52.883: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] -** Message: 14:30:52.889: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] -** Message: 14:30:52.891: Compiling codegen: +** Message: 23:21:18.496: Adding function [optimal_58_NER_58_affine_58_local_58_dna2dna_32_find_32_path_32_continuation] +** Message: 23:21:18.500: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:dna2dna]]] +** Message: 23:21:18.501: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:54.055: Compiling codegen: +** Message: 23:21:19.028: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:55.924: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:55.924: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:19.853: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:19.854: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:55.966: 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: 14:30:55.966: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:55.966: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:19.871: 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: 23:21:19.871: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:19.871: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:56.013: 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: 14:30:56.013: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] -** Message: 14:30:56.015: Compiling codegen: +** Message: 23:21:19.887: 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: 23:21:19.887: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:dna2dna]]] +** Message: 23:21:19.888: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:56.979: Compiling codegen: +** Message: 23:21:20.378: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:58.305: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:58.305: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:20.996: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:20.996: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:58.346: 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: 14:30:58.346: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:30:58.346: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:21.013: 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: 23:21:21.013: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:21.013: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:30:58.387: 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: 14:30:58.387: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] -** Message: 14:30:58.391: Compiling codegen: +** Message: 23:21:21.030: 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: 23:21:21.030: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:dna2dna]]] +** Message: 23:21:21.032: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:01.162: Compiling codegen: +** Message: 23:21:22.323: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:05.953: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:05.953: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:24.490: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:24.490: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:06.052: 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: 14:31:06.052: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:06.052: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:24.517: 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: 23:21:24.517: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:24.517: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:06.140: 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: 14:31:06.140: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] -** Message: 14:31:06.142: Compiling codegen: +** Message: 23:21:24.537: 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: 23:21:24.537: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] +** Message: 23:21:24.538: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:07.218: Compiling codegen: +** Message: 23:21:25.019: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:08.728: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:08.728: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:25.695: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:25.695: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:08.796: 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: 14:31:08.796: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:08.796: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:25.717: 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: 23:21:25.717: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:25.717: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:08.863: 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: 14:31:08.863: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] -** Message: 14:31:08.868: Compiling codegen: +** Message: 23:21:25.736: 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: 23:21:25.736: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:dna2dna]]] +** Message: 23:21:25.738: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:12.516: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:12.516: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:27.667: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:27.668: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:12.564: 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: 14:31:12.564: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] -** Message: 14:31:12.566: Compiling codegen: +** Message: 23:21:27.685: 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: 23:21:27.685: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:dna2dna]]] +** Message: 23:21:27.686: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:14.119: Compiling codegen: +** Message: 23:21:28.299: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:16.536: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:16.536: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:29.368: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:29.368: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:16.592: 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: 14:31:16.592: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:16.592: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:29.387: 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: 23:21:29.387: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:29.387: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:16.640: 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: 14:31:16.641: Compiling codegen: +** Message: 23:21:29.405: 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: 23:21:29.406: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.c -** Message: 14:31:17.253: Compiling codegen: +** Message: 23:21:29.648: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.c -** Message: 14:31:17.741: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] -** Message: 14:31:17.741: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:29.910: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o] +** Message: 23:21:29.910: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary.o -** Message: 14:31:17.788: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] -** Message: 14:31:17.788: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] -** Message: 14:31:17.788: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:29.930: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_reverse_58_notraceback_58_boundary] +** Message: 23:21:29.930: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o] +** Message: 23:21:29.930: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary.o -** Message: 14:31:17.832: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] -** Message: 14:31:17.832: Bootstrapper processing model [NER:affine:local:protein2protein] -** Message: 14:31:17.832: Process optimal [optimal:NER:affine:local:protein2protein] -** Message: 14:31:17.833: Compiling codegen: +** Message: 23:21:30.002: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_dna2dna_58_forward_58_traceback_58_boundary] +** Message: 23:21:30.002: Bootstrapper processing model [NER:affine:local:protein2protein] +** Message: 23:21:30.002: Process optimal [optimal:NER:affine:local:protein2protein] +** Message: 23:21:30.003: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.c -** Message: 14:31:18.377: Compiling codegen: +** Message: 23:21:30.256: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.c -** Message: 14:31:19.101: Compiling codegen: +** Message: 23:21:30.627: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.c -** Message: 14:31:19.747: Compiling codegen: +** Message: 23:21:30.973: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.c -** Message: 14:31:20.933: Compiling codegen: +** Message: 23:21:31.654: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.c -** Message: 14:31:22.412: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] -** Message: 14:31:22.412: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] to archive +** Message: 23:21:32.417: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o] +** Message: 23:21:32.417: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score.o -** Message: 14:31:22.476: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] -** Message: 14:31:22.476: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] -** Message: 14:31:22.476: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] to archive +** Message: 23:21:32.437: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_score] +** Message: 23:21:32.437: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o] +** Message: 23:21:32.437: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path.o -** Message: 14:31:22.531: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] -** Message: 14:31:22.531: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] -** Message: 14:31:22.531: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] to archive +** Message: 23:21:32.499: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path] +** Message: 23:21:32.499: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o] +** Message: 23:21:32.499: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region.o -** Message: 14:31:22.630: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] -** Message: 14:31:22.630: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] -** Message: 14:31:22.630: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] to archive +** Message: 23:21:32.518: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_region] +** Message: 23:21:32.518: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o] +** Message: 23:21:32.518: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint.o -** Message: 14:31:22.740: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] -** Message: 14:31:22.740: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] -** Message: 14:31:22.740: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:32.537: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_checkpoint] +** Message: 23:21:32.537: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o] +** Message: 23:21:32.537: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation.o -** Message: 14:31:22.844: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] -** Message: 14:31:22.850: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] -** Message: 14:31:22.856: Compiling codegen: +** Message: 23:21:32.557: Adding function [optimal_58_NER_58_affine_58_local_58_protein2protein_32_find_32_path_32_continuation] +** Message: 23:21:32.560: Process optimal [Terminal [Segment("START"->"match"):[NER:affine:local:protein2protein]]] +** Message: 23:21:32.561: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:23.982: Compiling codegen: +** Message: 23:21:33.098: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:25.476: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:25.476: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:34.434: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:34.434: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:25.556: 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: 14:31:25.556: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:25.556: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:34.455: 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: 23:21:34.455: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:34.455: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:25.626: 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: 14:31:25.626: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] -** Message: 14:31:25.628: Compiling codegen: +** Message: 23:21:34.475: 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: 23:21:34.475: Process optimal [Terminal [Segment("match"->"END"):[NER:affine:local:protein2protein]]] +** Message: 23:21:34.476: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:26.503: Compiling codegen: +** Message: 23:21:34.905: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:27.759: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:27.759: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:35.522: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:35.522: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:27.819: 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: 14:31:27.819: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:27.819: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:35.542: 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: 23:21:35.542: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:35.542: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:27.903: 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: 14:31:27.904: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] -** Message: 14:31:27.907: Compiling codegen: +** Message: 23:21:35.562: 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: 23:21:35.562: Process optimal [HeuristicJoin:[Segment("match"->"match"):[NER:affine:local:protein2protein]]] +** Message: 23:21:35.564: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:30.276: Compiling codegen: +** Message: 23:21:36.814: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:35.016: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:35.016: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:38.931: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:38.931: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:35.075: 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: 14:31:35.075: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:35.075: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:38.954: 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: 23:21:38.954: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:38.954: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:35.138: 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: 14:31:35.138: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] -** Message: 14:31:35.139: Compiling codegen: +** Message: 23:21:38.976: 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: 23:21:38.977: Process optimal [Src span [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] +** Message: 23:21:38.978: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:36.257: Compiling codegen: +** Message: 23:21:39.473: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:37.804: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:37.805: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:40.156: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:40.156: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:37.900: 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: 14:31:37.900: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:37.900: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:40.177: 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: 23:21:40.177: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:40.178: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:38.008: 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: 14:31:38.008: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] -** Message: 14:31:38.012: Compiling codegen: +** Message: 23:21:40.199: 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: 23:21:40.199: Process optimal [Src span traceback [Segment("match"->"ner"):[NER:affine:local:protein2protein]]] +** Message: 23:21:40.202: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:42.388: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:42.388: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:42.407: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:42.407: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:42.468: 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: 14:31:42.468: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] -** Message: 14:31:42.471: Compiling codegen: +** Message: 23:21:42.430: 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: 23:21:42.430: Process optimal [Dst span [Segment("ner"->"match"):[NER:affine:local:protein2protein]]] +** Message: 23:21:42.432: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:43.839: Compiling codegen: +** Message: 23:21:43.040: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:46.076: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:46.077: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:44.041: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:44.041: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:46.131: 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: 14:31:46.131: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:31:46.131: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:44.066: 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: 23:21:44.066: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:44.066: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:46.186: 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: 14:31:46.187: Compiling codegen: +** Message: 23:21:44.091: 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: 23:21:44.092: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.c -** Message: 14:31:46.720: Compiling codegen: +** Message: 23:21:44.328: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.c -** Message: 14:31:47.290: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] -** Message: 14:31:47.290: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:44.584: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o] +** Message: 23:21:44.584: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary.o -** Message: 14:31:47.341: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] -** Message: 14:31:47.341: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] -** Message: 14:31:47.341: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:44.607: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_reverse_58_notraceback_58_boundary] +** Message: 23:21:44.607: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o] +** Message: 23:21:44.607: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary.o -** Message: 14:31:47.407: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] -** Message: 14:31:47.407: Processing model [p2d] -** Message: 14:31:47.407: Bootstrapper processing model [protein2dna:local] -** Message: 14:31:47.407: Process optimal [optimal:protein2dna:local] -** Message: 14:31:47.408: Compiling codegen: +** Message: 23:21:44.629: Adding function [Scheduler_Cell_process_NER_58_affine_58_local_58_protein2protein_58_forward_58_traceback_58_boundary] +** Message: 23:21:44.629: Processing model [p2d] +** Message: 23:21:44.629: Bootstrapper processing model [protein2dna:local] +** Message: 23:21:44.629: Process optimal [optimal:protein2dna:local] +** Message: 23:21:44.630: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.c -** Message: 14:31:48.253: Compiling codegen: +** Message: 23:21:45.020: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.c -** Message: 14:31:49.526: Compiling codegen: +** Message: 23:21:45.566: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.c -** Message: 14:31:50.672: Compiling codegen: +** Message: 23:21:46.274: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.c -** Message: 14:31:53.683: Compiling codegen: +** Message: 23:21:48.040: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.c -** Message: 14:31:56.957: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] -** Message: 14:31:56.957: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] to archive +** Message: 23:21:49.545: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o] +** Message: 23:21:49.545: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_score.o -** Message: 14:31:57.014: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] -** Message: 14:31:57.014: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] -** Message: 14:31:57.014: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] to archive +** Message: 23:21:49.568: Adding function [optimal_58_protein2dna_58_local_32_find_32_score] +** Message: 23:21:49.568: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o] +** Message: 23:21:49.568: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path.o -** Message: 14:31:57.092: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] -** Message: 14:31:57.092: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] -** Message: 14:31:57.092: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] to archive +** Message: 23:21:49.592: Adding function [optimal_58_protein2dna_58_local_32_find_32_path] +** Message: 23:21:49.592: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o] +** Message: 23:21:49.592: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_region.o -** Message: 14:31:57.167: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] -** Message: 14:31:57.168: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] -** Message: 14:31:57.168: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] to archive +** Message: 23:21:49.616: Adding function [optimal_58_protein2dna_58_local_32_find_32_region] +** Message: 23:21:49.616: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o] +** Message: 23:21:49.616: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_checkpoint.o -** Message: 14:31:57.249: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] -** Message: 14:31:57.249: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] -** Message: 14:31:57.249: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] to archive +** Message: 23:21:49.641: Adding function [optimal_58_protein2dna_58_local_32_find_32_checkpoint] +** Message: 23:21:49.642: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o] +** Message: 23:21:49.642: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_local_32_find_32_path_32_continuation.o -** Message: 14:31:57.352: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] -** Message: 14:31:57.367: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] -** Message: 14:31:57.371: Compiling codegen: +** Message: 23:21:49.667: Adding function [optimal_58_protein2dna_58_local_32_find_32_path_32_continuation] +** Message: 23:21:49.674: Process optimal [Terminal [Segment("START"->"match"):[protein2dna:local]]] +** Message: 23:21:49.676: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:31:59.588: Compiling codegen: +** Message: 23:21:50.660: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:32:03.316: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:32:03.316: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:52.288: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:52.289: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:32:03.378: 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: 14:32:03.378: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:32:03.378: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:52.312: 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: 23:21:52.312: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:52.312: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:32:03.447: 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: 14:32:03.447: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] -** Message: 14:32:03.449: Compiling codegen: +** Message: 23:21:52.335: 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: 23:21:52.335: Process optimal [Terminal [Segment("match"->"END"):[protein2dna:local]]] +** Message: 23:21:52.336: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:32:04.854: Compiling codegen: +** Message: 23:21:52.978: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:32:06.853: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:32:06.853: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:54.017: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:54.017: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:32:06.920: 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: 14:32:06.920: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:32:06.920: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:54.041: 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: 23:21:54.041: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:54.041: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:32:07.000: 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: 14:32:07.000: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] -** Message: 14:32:07.009: Compiling codegen: +** Message: 23:21:54.065: 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: 23:21:54.065: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2dna:local]]] +** Message: 23:21:54.068: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:32:11.538: Compiling codegen: +** Message: 23:21:56.033: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:32:19.233: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:32:19.233: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:59.457: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:59.457: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:32:19.616: 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: 14:32:19.616: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:32:19.616: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:21:59.482: 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: 23:21:59.482: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:21:59.482: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:32:19.732: 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: 14:32:19.733: Compiling codegen: +** Message: 23:21:59.580: 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: 23:21:59.581: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.c -** Message: 14:32:20.388: Compiling codegen: +** Message: 23:21:59.844: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.c -** Message: 14:32:21.005: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] -** Message: 14:32:21.005: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] to archive +** Message: 23:22:00.110: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o] +** Message: 23:22:00.110: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded.o -** Message: 14:32:21.068: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] -** Message: 14:32:21.068: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] -** Message: 14:32:21.068: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] to archive +** Message: 23:22:00.136: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_reverse_58_traceback_58_seeded] +** Message: 23:22:00.136: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o] +** Message: 23:22:00.136: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded.o -** Message: 14:32:21.124: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] -** Message: 14:32:21.124: Processing model [p2d:b] -** Message: 14:32:21.125: Bootstrapper processing model [protein2dna:bestfit] -** Message: 14:32:21.125: Process optimal [optimal:protein2dna:bestfit] -** Message: 14:32:21.129: Compiling codegen: +** Message: 23:22:00.161: Adding function [Scheduler_Cell_process_protein2dna_58_local_58_forward_58_traceback_58_seeded] +** Message: 23:22:00.161: Processing model [p2d:b] +** Message: 23:22:00.162: Bootstrapper processing model [protein2dna:bestfit] +** Message: 23:22:00.162: Process optimal [optimal:protein2dna:bestfit] +** Message: 23:22:00.164: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.c -** Message: 14:32:23.846: Compiling codegen: +** Message: 23:22:01.338: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.c -** Message: 14:32:28.410: Compiling codegen: +** Message: 23:22:03.349: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.c -** Message: 14:32:32.718: Compiling codegen: +** Message: 23:22:05.243: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.c -** Message: 14:32:35.971: Compiling codegen: +** Message: 23:22:06.737: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.c -** Message: 14:32:39.387: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] -** Message: 14:32:39.387: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] to archive +** Message: 23:22:08.834: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o] +** Message: 23:22:08.834: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_score.o -** Message: 14:32:39.456: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] -** Message: 14:32:39.456: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] -** Message: 14:32:39.456: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] to archive +** Message: 23:22:08.945: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_score] +** Message: 23:22:08.945: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o] +** Message: 23:22:08.945: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path.o -** Message: 14:32:39.519: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] -** Message: 14:32:39.519: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] -** Message: 14:32:39.519: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] to archive +** Message: 23:22:09.074: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path] +** Message: 23:22:09.074: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o] +** Message: 23:22:09.074: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_region.o -** Message: 14:32:39.583: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] -** Message: 14:32:39.583: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] -** Message: 14:32:39.583: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] to archive +** Message: 23:22:09.220: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_region] +** Message: 23:22:09.220: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o] +** Message: 23:22:09.220: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint.o -** Message: 14:32:39.669: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] -** Message: 14:32:39.669: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] -** Message: 14:32:39.669: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] to archive +** Message: 23:22:09.356: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_checkpoint] +** Message: 23:22:09.357: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o] +** Message: 23:22:09.357: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation.o -** Message: 14:32:39.764: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] -** Message: 14:32:39.764: Processing model [p2g] -** Message: 14:32:39.765: Bootstrapper processing model [protein2genome:local] -** Message: 14:32:39.765: Process optimal [optimal:protein2genome:local] -** Message: 14:32:39.772: Compiling codegen: +** Message: 23:22:09.400: Adding function [optimal_58_protein2dna_58_bestfit_32_find_32_path_32_continuation] +** Message: 23:22:09.400: Processing model [p2g] +** Message: 23:22:09.400: Bootstrapper processing model [protein2genome:local] +** Message: 23:22:09.400: Process optimal [optimal:protein2genome:local] +** Message: 23:22:09.402: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.c -** Message: 14:32:42.452: Compiling codegen: +** Message: 23:22:10.662: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.c -** Message: 14:32:46.673: Compiling codegen: +** Message: 23:22:12.471: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.c -** Message: 14:32:51.470: Compiling codegen: +** Message: 23:22:14.063: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.c -** Message: 14:33:15.676: Compiling codegen: +** Message: 23:22:19.660: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.c -** Message: 14:33:43.832: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] -** Message: 14:33:43.832: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] to archive +** Message: 23:22:29.486: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o] +** Message: 23:22:29.486: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_score.o -** Message: 14:33:43.961: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] -** Message: 14:33:43.961: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] -** Message: 14:33:43.961: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] to archive +** Message: 23:22:29.530: Adding function [optimal_58_protein2genome_58_local_32_find_32_score] +** Message: 23:22:29.530: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o] +** Message: 23:22:29.530: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path.o -** Message: 14:33:44.092: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] -** Message: 14:33:44.092: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] -** Message: 14:33:44.092: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] to archive +** Message: 23:22:29.573: Adding function [optimal_58_protein2genome_58_local_32_find_32_path] +** Message: 23:22:29.573: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o] +** Message: 23:22:29.573: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_region.o -** Message: 14:33:44.232: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] -** Message: 14:33:44.232: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] -** Message: 14:33:44.232: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] to archive +** Message: 23:22:29.617: Adding function [optimal_58_protein2genome_58_local_32_find_32_region] +** Message: 23:22:29.617: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o] +** Message: 23:22:29.617: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_checkpoint.o -** Message: 14:33:44.321: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] -** Message: 14:33:44.321: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] -** Message: 14:33:44.321: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] to archive +** Message: 23:22:29.660: Adding function [optimal_58_protein2genome_58_local_32_find_32_checkpoint] +** Message: 23:22:29.660: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o] +** Message: 23:22:29.660: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_local_32_find_32_path_32_continuation.o -** Message: 14:33:44.415: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] -** Message: 14:33:44.479: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] -** Message: 14:33:44.500: Compiling codegen: +** Message: 23:22:29.713: Adding function [optimal_58_protein2genome_58_local_32_find_32_path_32_continuation] +** Message: 23:22:29.755: Process optimal [Terminal [Segment("START"->"match"):[protein2genome:local]]] +** Message: 23:22:29.763: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:33:58.471: Compiling codegen: +** Message: 23:22:39.263: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:34:30.500: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:34:30.500: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:22:53.862: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:22:53.862: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:34:30.641: 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: 14:34:30.641: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:34:30.641: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:22:53.906: 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: 23:22:53.906: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:22:53.906: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:34:30.796: 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: 14:34:30.796: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] -** Message: 14:34:30.801: Compiling codegen: +** Message: 23:22:53.951: 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: 23:22:53.952: Process optimal [Terminal [Segment("match"->"END"):[protein2genome:local]]] +** Message: 23:22:53.956: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:34:37.046: Compiling codegen: +** Message: 23:22:57.653: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:34:50.860: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:34:50.860: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:23:01.478: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:23:01.478: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:34:50.968: 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: 14:34:50.968: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:34:50.968: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:23:01.511: 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: 23:23:01.511: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:23:01.511: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:34:51.052: 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: 14:34:51.052: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] -** Message: 14:34:51.073: Compiling codegen: +** Message: 23:23:01.542: 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: 23:23:01.542: Process optimal [HeuristicJoin:[Segment("match"->"match"):[protein2genome:local]]] +** Message: 23:23:01.556: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:35:19.824: Compiling codegen: +** Message: 23:23:12.018: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:36:13.524: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:36:13.524: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:23:33.502: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:23:33.502: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:36:13.596: 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: 14:36:13.596: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:36:13.596: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:23:33.541: 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: 23:23:33.541: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:23:33.541: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:36:13.697: 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: 14:36:13.697: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] -** Message: 14:36:13.702: Compiling codegen: +** Message: 23:23:33.575: 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: 23:23:33.575: Process optimal [Src span [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] +** Message: 23:23:33.577: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:36:19.023: Compiling codegen: +** Message: 23:23:35.841: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:36:27.478: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:36:27.478: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:23:39.652: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:23:39.652: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:36:27.584: 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: 14:36:27.584: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:36:27.584: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:23:39.687: 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: 23:23:39.687: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:23:39.687: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:36:27.689: 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: 14:36:27.689: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] -** Message: 14:36:27.711: Compiling codegen: +** Message: 23:23:39.721: 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: 23:23:39.721: Process optimal [Src span traceback [Segment("match"->"intron 0:0 phase-T"):[protein2genome:local]]] +** Message: 23:23:39.728: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:37:09.880: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:37:09.880: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:23:56.443: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:23:56.443: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:37:10.052: 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: 14:37:10.052: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] -** Message: 14:37:10.059: Compiling codegen: +** Message: 23:23:56.476: 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: 23:23:56.476: Process optimal [Dst span [Segment("intron 0:0 phase-T"->"match"):[protein2genome:local]]] +** Message: 23:23:56.480: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:37:20.680: Compiling codegen: +** Message: 23:24:00.924: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:37:39.112: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:37:39.112: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:24:09.947: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:24:09.947: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:37:39.240: 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: 14:37:39.240: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:37:39.240: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:24:09.983: 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: 23:24:09.983: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:24:09.983: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:37:39.352: 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: 14:37:39.352: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] -** Message: 14:37:39.357: Compiling codegen: +** Message: 23:24:10.050: 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: 23:24:10.050: Process optimal [Src span [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] +** Message: 23:24:10.054: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:37:44.650: Compiling codegen: +** Message: 23:24:12.347: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:37:54.324: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:37:54.324: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:24:16.817: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:24:16.817: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:37:54.524: 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: 14:37:54.524: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:37:54.524: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:24:16.896: 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: 23:24:16.896: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:24:16.896: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:37:54.728: 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: 14:37:54.728: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] -** Message: 14:37:54.751: Compiling codegen: +** Message: 23:24:17.022: 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: 23:24:17.022: Process optimal [Src span traceback [Segment("match"->"intron 1:2 phase-T"):[protein2genome:local]]] +** Message: 23:24:17.035: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:38:34.976: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:38:34.976: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:24:33.701: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:24:33.702: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:38:35.168: 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: 14:38:35.168: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] -** Message: 14:38:35.181: Compiling codegen: +** Message: 23:24:33.738: 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: 23:24:33.738: Process optimal [Dst span [Segment("intron 1:2 phase-T"->"match"):[protein2genome:local]]] +** Message: 23:24:33.743: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:38:46.087: Compiling codegen: +** Message: 23:24:38.187: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:39:06.848: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:39:06.848: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:24:47.044: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:24:47.045: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:39:06.988: 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: 14:39:06.988: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:39:06.988: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:24:47.086: 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: 23:24:47.086: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:24:47.086: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:39:07.416: 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: 14:39:07.416: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] -** Message: 14:39:07.420: Compiling codegen: +** Message: 23:24:47.133: 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: 23:24:47.133: Process optimal [Src span [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] +** Message: 23:24:47.136: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:39:12.628: Compiling codegen: +** Message: 23:24:49.394: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:39:21.200: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:39:21.200: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:24:53.206: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:24:53.206: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:39:21.380: 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: 14:39:21.380: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:39:21.380: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:24:53.250: 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: 23:24:53.250: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:24:53.250: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:39:21.524: 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: 14:39:21.524: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] -** Message: 14:39:21.539: Compiling codegen: +** Message: 23:24:53.298: 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: 23:24:53.298: Process optimal [Src span traceback [Segment("match"->"intron 2:1 phase-T"):[protein2genome:local]]] +** Message: 23:24:53.305: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:40:00.149: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:40:00.149: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:25:10.365: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:25:10.365: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:40:00.231: 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: 14:40:00.231: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] -** Message: 14:40:00.238: Compiling codegen: +** Message: 23:25:10.403: 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: 23:25:10.403: Process optimal [Dst span [Segment("intron 2:1 phase-T"->"match"):[protein2genome:local]]] +** Message: 23:25:10.407: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:40:11.124: Compiling codegen: +** Message: 23:25:14.843: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:40:31.232: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:40:31.232: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:25:23.653: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:25:23.653: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:40:31.500: 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: 14:40:31.500: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:40:31.500: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:25:23.705: 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: 23:25:23.705: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:25:23.705: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:40:31.668: 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: 14:40:31.670: Compiling codegen: +** Message: 23:25:23.752: 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: 23:25:23.753: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.c -** Message: 14:40:32.701: Compiling codegen: +** Message: 23:25:24.197: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.c -** Message: 14:40:33.792: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] -** Message: 14:40:33.792: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] to archive +** Message: 23:25:24.655: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o] +** Message: 23:25:24.655: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary.o -** Message: 14:40:33.956: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] -** Message: 14:40:33.956: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] -** Message: 14:40:33.956: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] to archive +** Message: 23:25:24.694: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_reverse_58_notraceback_58_boundary] +** Message: 23:25:24.694: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o] +** Message: 23:25:24.694: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary.o -** Message: 14:40:34.060: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] -** Message: 14:40:34.060: Processing model [p2g:b] -** Message: 14:40:34.061: Bootstrapper processing model [protein2genome:bestfit] -** Message: 14:40:34.061: Process optimal [optimal:protein2genome:bestfit] -** Message: 14:40:34.072: Compiling codegen: +** Message: 23:25:24.775: Adding function [Scheduler_Cell_process_protein2genome_58_local_58_forward_58_traceback_58_boundary] +** Message: 23:25:24.775: Processing model [p2g:b] +** Message: 23:25:24.776: Bootstrapper processing model [protein2genome:bestfit] +** Message: 23:25:24.776: Process optimal [optimal:protein2genome:bestfit] +** Message: 23:25:24.781: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.c -** Message: 14:40:46.411: Compiling codegen: +** Message: 23:25:30.176: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.c -** Message: 14:41:16.081: Compiling codegen: +** Message: 23:25:40.962: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.c -** Message: 14:41:33.638: Compiling codegen: +** Message: 23:25:47.994: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.c -** Message: 14:41:42.617: Compiling codegen: +** Message: 23:25:53.041: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.c -** Message: 14:41:54.165: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] -** Message: 14:41:54.165: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] to archive +** Message: 23:25:59.877: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o] +** Message: 23:25:59.878: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_score.o -** Message: 14:41:54.560: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] -** Message: 14:41:54.560: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] -** Message: 14:41:54.560: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] to archive +** Message: 23:25:59.922: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_score] +** Message: 23:25:59.922: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o] +** Message: 23:25:59.922: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path.o -** Message: 14:41:54.659: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] -** Message: 14:41:54.692: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] -** Message: 14:41:54.692: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] to archive +** Message: 23:25:59.965: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path] +** Message: 23:25:59.965: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o] +** Message: 23:25:59.965: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_region.o -** Message: 14:41:54.820: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] -** Message: 14:41:54.820: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] -** Message: 14:41:54.820: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] to archive +** Message: 23:26:00.008: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_region] +** Message: 23:26:00.008: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o] +** Message: 23:26:00.008: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint.o -** Message: 14:41:54.924: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] -** Message: 14:41:54.924: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] -** Message: 14:41:54.924: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] to archive +** Message: 23:26:00.052: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_checkpoint] +** Message: 23:26:00.052: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o] +** Message: 23:26:00.052: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation.o -** Message: 14:41:55.072: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] -** Message: 14:41:55.072: Processing model [c2c] -** Message: 14:41:55.073: Bootstrapper processing model [coding2coding] -** Message: 14:41:55.073: Process optimal [optimal:coding2coding] -** Message: 14:41:55.080: Compiling codegen: +** Message: 23:26:00.129: Adding function [optimal_58_protein2genome_58_bestfit_32_find_32_path_32_continuation] +** Message: 23:26:00.129: Processing model [c2c] +** Message: 23:26:00.130: Bootstrapper processing model [coding2coding] +** Message: 23:26:00.130: Process optimal [optimal:coding2coding] +** Message: 23:26:00.133: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.c -** Message: 14:41:56.571: Compiling codegen: +** Message: 23:26:00.999: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.c -** Message: 14:41:59.532: Compiling codegen: +** Message: 23:26:02.350: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.c -** Message: 14:42:03.152: Compiling codegen: +** Message: 23:26:03.969: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.c -** Message: 14:42:10.445: Compiling codegen: +** Message: 23:26:08.185: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.c -** Message: 14:42:22.848: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] -** Message: 14:42:22.848: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] to archive +** Message: 23:26:12.732: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] +** Message: 23:26:12.732: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_score.o -** Message: 14:42:23.028: Adding function [optimal_58_coding2coding_32_find_32_score] -** Message: 14:42:23.028: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] -** Message: 14:42:23.028: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] to archive +** Message: 23:26:12.782: Adding function [optimal_58_coding2coding_32_find_32_score] +** Message: 23:26:12.782: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] +** Message: 23:26:12.782: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path.o -** Message: 14:42:23.176: Adding function [optimal_58_coding2coding_32_find_32_path] -** Message: 14:42:23.176: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] -** Message: 14:42:23.176: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] to archive +** Message: 23:26:12.830: Adding function [optimal_58_coding2coding_32_find_32_path] +** Message: 23:26:12.830: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] +** Message: 23:26:12.830: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_region.o -** Message: 14:42:23.376: Adding function [optimal_58_coding2coding_32_find_32_region] -** Message: 14:42:23.376: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] -** Message: 14:42:23.376: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive +** Message: 23:26:12.879: Adding function [optimal_58_coding2coding_32_find_32_region] +** Message: 23:26:12.879: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] +** Message: 23:26:12.879: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_checkpoint.o -** Message: 14:42:23.544: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] -** Message: 14:42:23.544: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] -** Message: 14:42:23.544: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] to archive +** Message: 23:26:12.954: Adding function [optimal_58_coding2coding_32_find_32_checkpoint] +** Message: 23:26:12.954: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o] +** Message: 23:26:12.954: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2coding_32_find_32_path_32_continuation.o -** Message: 14:42:23.720: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] -** Message: 14:42:23.792: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] -** Message: 14:42:23.805: Compiling codegen: +** Message: 23:26:12.998: Adding function [optimal_58_coding2coding_32_find_32_path_32_continuation] +** Message: 23:26:13.023: Process optimal [Terminal [Segment("START"->"match"):[coding2coding]]] +** Message: 23:26:13.027: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:42:33.226: Compiling codegen: +** Message: 23:26:15.816: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:42:49.830: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:42:49.830: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:26:21.257: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:26:21.257: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:42:49.989: 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: 14:42:49.989: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:42:49.989: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:26:21.310: 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: 23:26:21.310: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:26:21.310: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:42:50.196: 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: 14:42:50.196: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] -** Message: 14:42:50.199: Compiling codegen: +** Message: 23:26:21.374: 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: 23:26:21.374: Process optimal [Terminal [Segment("match"->"END"):[coding2coding]]] +** Message: 23:26:21.376: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:42:53.779: Compiling codegen: +** Message: 23:26:22.792: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:42:59.528: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:42:59.528: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:26:24.978: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:26:24.978: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:42:59.696: 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: 14:42:59.696: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:42:59.696: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:26:25.041: 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: 23:26:25.041: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:26:25.041: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:42:59.928: 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: 14:42:59.928: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] -** Message: 14:42:59.956: Compiling codegen: +** Message: 23:26:25.097: 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: 23:26:25.097: Process optimal [HeuristicJoin:[Segment("match"->"match"):[coding2coding]]] +** Message: 23:26:25.103: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:43:12.324: Compiling codegen: +** Message: 23:26:30.569: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:43:42.592: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:43:42.592: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:26:41.396: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:26:41.396: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:43:42.788: 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: 14:43:42.788: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 14:43:42.788: Adding object file [/build/exonerate-2.4.0/codegen/i686_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: 23:26:41.454: 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: 23:26:41.454: Adding: [/build/exonerate-2.4.0/codegen/i686_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: 23:26:41.454: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_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: 14:43:42.956: 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: 14:43:42.957: Compiling codegen: +** Message: 23:26:41.509: 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: 23:26:41.510: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.c -** Message: 14:43:43.891: Compiling codegen: +** Message: 23:26:41.836: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.c -** Message: 14:43:45.280: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] -** Message: 14:43:45.281: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] to archive +** Message: 23:26:42.161: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o] +** Message: 23:26:42.161: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded.o -** Message: 14:43:45.408: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] -** Message: 14:43:45.408: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] -** Message: 14:43:45.408: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] to archive +** Message: 23:26:42.207: Adding function [Scheduler_Cell_process_coding2coding_58_reverse_58_traceback_58_seeded] +** Message: 23:26:42.207: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o] +** Message: 23:26:42.207: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded.o -** Message: 14:43:45.533: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] -** Message: 14:43:45.533: Processing model [c2g] -** Message: 14:43:45.535: Bootstrapper processing model [coding2genome] -** Message: 14:43:45.535: Process optimal [optimal:coding2genome] -** Message: 14:43:45.543: Compiling codegen: +** Message: 23:26:42.253: Adding function [Scheduler_Cell_process_coding2coding_58_forward_58_traceback_58_seeded] +** Message: 23:26:42.253: Processing model [c2g] +** Message: 23:26:42.254: Bootstrapper processing model [coding2genome] +** Message: 23:26:42.254: Process optimal [optimal:coding2genome] +** Message: 23:26:42.257: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.c -** Message: 14:43:53.864: Compiling codegen: +** Message: 23:26:45.170: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.c -** Message: 14:44:07.891: Compiling codegen: +** Message: 23:26:51.033: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.c -** Message: 14:44:20.171: Compiling codegen: +** Message: 23:26:56.893: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.c -** Message: 14:45:13.256: Compiling codegen: +** Message: 23:27:17.304: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.c -** Message: 14:46:37.508: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] -** Message: 14:46:37.508: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] to archive +** Message: 23:27:47.930: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] +** Message: 23:27:47.931: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_score.o -** Message: 14:46:37.660: Adding function [optimal_58_coding2genome_32_find_32_score] -** Message: 14:46:37.660: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] -** Message: 14:46:37.660: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] to archive +** Message: 23:27:47.992: Adding function [optimal_58_coding2genome_32_find_32_score] +** Message: 23:27:47.992: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] +** Message: 23:27:47.992: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path.o -** Message: 14:46:37.832: Adding function [optimal_58_coding2genome_32_find_32_path] -** Message: 14:46:37.832: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] -** Message: 14:46:37.832: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] to archive +** Message: 23:27:48.053: Adding function [optimal_58_coding2genome_32_find_32_path] +** Message: 23:27:48.054: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] +** Message: 23:27:48.054: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_region.o -** Message: 14:46:37.968: Adding function [optimal_58_coding2genome_32_find_32_region] -** Message: 14:46:37.968: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] -** Message: 14:46:37.968: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive +** Message: 23:27:48.118: Adding function [optimal_58_coding2genome_32_find_32_region] +** Message: 23:27:48.118: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] +** Message: 23:27:48.118: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_checkpoint.o -** Message: 14:46:38.120: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] -** Message: 14:46:38.120: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] -** Message: 14:46:38.120: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] to archive +** Message: 23:27:48.181: Adding function [optimal_58_coding2genome_32_find_32_checkpoint] +** Message: 23:27:48.181: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o] +** Message: 23:27:48.181: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_coding2genome_32_find_32_path_32_continuation.o -** Message: 14:46:38.268: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] -** Message: 14:46:38.270: Compiling codegen: +** Message: 23:27:48.248: Adding function [optimal_58_coding2genome_32_find_32_path_32_continuation] +** Message: 23:27:48.249: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.c -** Message: 14:46:39.200: Compiling codegen: +** Message: 23:27:48.720: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.c -** Message: 14:46:40.864: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] -** Message: 14:46:40.864: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] to archive +** Message: 23:27:49.279: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o] +** Message: 23:27:49.279: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary.o -** Message: 14:46:41.084: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] -** Message: 14:46:41.084: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] -** Message: 14:46:41.084: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] to archive +** Message: 23:27:49.334: Adding function [Scheduler_Cell_process_coding2genome_58_reverse_58_notraceback_58_boundary] +** Message: 23:27:49.334: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o] +** Message: 23:27:49.334: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary.o -** Message: 14:46:41.328: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] -** Message: 14:46:41.328: Processing model [cd2g] -** Message: 14:46:41.331: Bootstrapper processing model [cdna2genome] -** Message: 14:46:41.331: Process optimal [optimal:cdna2genome] -** Message: 14:46:41.356: Compiling codegen: +** Message: 23:27:49.409: Adding function [Scheduler_Cell_process_coding2genome_58_forward_58_traceback_58_boundary] +** Message: 23:27:49.409: Processing model [cd2g] +** Message: 23:27:49.410: Bootstrapper processing model [cdna2genome] +** Message: 23:27:49.410: Process optimal [optimal:cdna2genome] +** Message: 23:27:49.416: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.c -** Message: 14:47:01.005: Compiling codegen: +** Message: 23:28:01.247: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.c -** Message: 14:47:52.639: Compiling codegen: +** Message: 23:28:19.490: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.c -** Message: 14:48:33.791: Compiling codegen: +** Message: 23:28:40.568: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.c -** Message: 14:51:00.720: Compiling codegen: +** Message: 23:30:53.847: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.c -** Message: 14:55:12.662: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] -** Message: 14:55:12.662: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] to archive +** Message: 23:33:14.290: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] +** Message: 23:33:14.290: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_score.o -** Message: 14:55:13.042: Adding function [optimal_58_cdna2genome_32_find_32_score] -** Message: 14:55:13.042: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] -** Message: 14:55:13.042: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] to archive +** Message: 23:33:14.398: Adding function [optimal_58_cdna2genome_32_find_32_score] +** Message: 23:33:14.398: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] +** Message: 23:33:14.398: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path.o -** Message: 14:55:13.204: Adding function [optimal_58_cdna2genome_32_find_32_path] -** Message: 14:55:13.204: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] -** Message: 14:55:13.204: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] to archive +** Message: 23:33:14.467: Adding function [optimal_58_cdna2genome_32_find_32_path] +** Message: 23:33:14.467: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] +** Message: 23:33:14.467: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_region.o -** Message: 14:55:13.367: Adding function [optimal_58_cdna2genome_32_find_32_region] -** Message: 14:55:13.368: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] -** Message: 14:55:13.368: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive +** Message: 23:33:14.543: Adding function [optimal_58_cdna2genome_32_find_32_region] +** Message: 23:33:14.543: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] +** Message: 23:33:14.543: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o] to archive ar -Sq c4_model_archive.a /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_checkpoint.o -** Message: 14:55:13.892: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] -** Message: 14:55:13.892: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] -** Message: 14:55:13.892: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] to archive +** Message: 23:33:14.637: Adding function [optimal_58_cdna2genome_32_find_32_checkpoint] +** Message: 23:33:14.637: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o] +** Message: 23:33:14.637: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/optimal_58_cdna2genome_32_find_32_path_32_continuation.o -** Message: 14:55:14.053: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] -** Message: 14:55:14.055: Compiling codegen: +** Message: 23:33:14.742: Adding function [optimal_58_cdna2genome_32_find_32_path_32_continuation] +** Message: 23:33:14.744: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.c -** Message: 14:55:16.654: Compiling codegen: +** Message: 23:33:15.539: Compiling codegen: gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/struct -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/sequence -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I/build/exonerate-2.4.0/src/model -I/build/exonerate-2.4.0/src/comparison -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/bsdp -I/build/exonerate-2.4.0/src/sdp -o /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c -** Message: 14:55:18.960: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] -** Message: 14:55:18.960: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive +** Message: 23:33:16.437: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] +** Message: 23:33:16.437: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o -** Message: 14:55:19.192: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] -** Message: 14:55:19.192: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] -** Message: 14:55:19.192: Adding object file [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive +** Message: 23:33:16.501: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary] +** Message: 23:33:16.502: Adding: [/build/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] +** Message: 23:33:16.502: Adding object file [/build/exonerate-2.4.0/codegen/i686_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/exonerate-2.4.0/codegen/i686_45_pc_45_linux_45_gnu/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -** Message: 14:55:19.354: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] -** Message: 14:55:19.360: Compiling with: [gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/sequence -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/struct -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -o c4_model_lookup.o -c c4_model_lookup.c] -** Message: 14:55:20.180: Adding: [c4_model_lookup.o] -** Message: 14:55:20.180: Adding object file [c4_model_lookup.o] to archive +** Message: 23:33:16.586: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary] +** Message: 23:33:16.586: Compiling with: [gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/build/exonerate-2.4.0/src/c4 -I/build/exonerate-2.4.0/src/sequence -I/build/exonerate-2.4.0/src/general -I/build/exonerate-2.4.0/src/struct -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -o c4_model_lookup.o -c c4_model_lookup.c] +** Message: 23:33:16.865: Adding: [c4_model_lookup.o] +** Message: 23:33:16.865: Adding object file [c4_model_lookup.o] to archive ar -Sq c4_model_archive.a c4_model_lookup.o -** Message: 14:55:20.388: Indexing archive [c4_model_archive.a] +** Message: 23:33:16.931: Indexing archive [c4_model_archive.a] ranlib c4_model_archive.a -** Message: 14:55:20.772: Done -** Message: 14:55:20.772: Finished building bootstrapping components +** Message: 23:33:17.049: Done +** Message: 23:33:17.050: Finished building bootstrapping components make all-am make[4]: Entering directory '/build/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="\"i686-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 @@ -2834,16 +2877,6 @@ -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="\"i686-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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="\"i686-pc-linux-gnu\"" -DSOURCE_ROOT_DIR="\"/build/exonerate-2.4.0\"" -DCUSTOM_GUINT64_FORMAT="\"llu\"" -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -exonerate-server.c:354:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" - 354 | g_string_sprintfa(str, " %d %d %d", - | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -exonerate-server.c:357:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" - 357 | g_string_sprintfa(str, "\n"); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ipcress.c: In function 'Ipcress_prepare_PCR': ipcress.c:264:9: warning: 'g_strup' is deprecated [-Wdeprecated-declarations] 264 | g_strup(primer_a); @@ -2859,6 +2892,16 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:212:23: note: declared here 212 | 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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +exonerate-server.c:354:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" + 354 | g_string_sprintfa(str, " %d %d %d", + | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +exonerate-server.c:357:13: warning: Deprecated pre-processor symbol: replace with "g_string_append_printf" + 357 | g_string_sprintfa(str, "\n"); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 ipcress ipcress.o ../../src/comparison/pcr.o ../../src/comparison/wordhood.o ../../src/database/fastadb.o ../../src/sequence/alphabet.o ../../src/sequence/sequence.o ../../src/sequence/splice.o ../../src/sequence/translate.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/struct/fsm.o ../../src/struct/slist.o ../../src/struct/matrix.o ../../src/struct/recyclebin.o ../../src/struct/sparsecache.o ../../src/general/lineparse.o ../../src/general/argument.o ../../src/general/compoundfile.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 exonerate-server exonerate-server.o ../../src/general/socket.o ../../src/general/argument.o ../../src/comparison/hspset.o ../../src/comparison/match.o ../../src/comparison/wordhood.o ../../src/database/dataset.o ../../src/database/index.o ../../src/database/fastadb.o ../../src/struct/bitarray.o ../../src/struct/sparsecache.o ../../src/struct/matrix.o ../../src/struct/splaytree.o ../../src/struct/noitree.o ../../src/struct/vfsm.o ../../src/struct/pqueue.o ../../src/struct/rangetree.o ../../src/struct/recyclebin.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o ../../src/general/compoundfile.o ../../src/general/lineparse.o ../../src/general/threadref.o -lm -lglib-2.0 gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 exonerate exonerate.o viterbi.o scheduler.o c4_model_archive.a ../../src/comparison/wordhood.o ../../src/comparison/hspset.o ../../src/comparison/seeder.o ../../src/comparison/comparison.o ../../src/database/fastapipe.o ../../src/database/fastadb.o ../../src/struct/dejavu.o ../../src/struct/fsm.o ../../src/struct/vfsm.o ../../src/struct/sparsecache.o ../../src/hub/gam.o ../../src/hub/bsam.o ../../src/hub/analysis.o ../../src/general/compoundfile.o ../../src/general/threadref.o ../../src/c4/c4.o ../../src/c4/codegen.o ../../src/c4/cgutil.o ../../src/c4/opair.o ../../src/c4/alignment.o ../../src/c4/optimal.o ../../src/c4/layout.o ../../src/c4/region.o ../../src/c4/subopt.o ../../src/bsdp/bsdp.o ../../src/bsdp/sar.o ../../src/bsdp/heuristic.o ../../src/bsdp/hpair.o ../../src/sdp/boundary.o ../../src/sdp/sdp.o ../../src/sdp/lookahead.o ../../src/sdp/straceback.o ../../src/struct/matrix.o ../../src/struct/slist.o ../../src/struct/pqueue.o ../../src/struct/recyclebin.o ../../src/struct/rangetree.o ../../src/sequence/sequence.o ../../src/sequence/alphabet.o ../../src/sequence/translate.o ../../src/sequence/splice.o ../../src/model/affine.o ../../src/model/est2genome.o ../../src/model/ner.o ../../src/model/protein2dna.o ../../src/model/protein2genome.o ../../src/model/coding2coding.o ../../src/model/coding2genome.o ../../src/model/cdna2genome.o ../../src/model/genome2genome.o ../../src/model/ungapped.o ../../src/model/intron.o ../../src/model/frameshift.o ../../src/model/phase.o ../../src/model/modeltype.o ../../src/general/argument.o ../../src/general/lineparse.o ../../src/general/socket.o ../../src/general/jobqueue.o ../../src/comparison/match.o ../../src/sequence/submat.o ../../src/sequence/codonsubmat.o -lm -lglib-2.0 @@ -2874,18 +2917,13 @@ 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaexplode.o fastaexplode.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastafetch.o fastafetch.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastahardmask.o fastahardmask.c -fastafetch.c: In function 'get_query_list': -fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] - 121 | if(!g_strcasecmp(query, "stdin")){ - | ^~ -In file included from /usr/include/glib-2.0/glib.h:84, - from ../../src/general/argument.h:26, - from fastafetch.c:21: -/usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here - 203 | 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaindex.o fastaindex.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastalength.o fastalength.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastanrdb.o fastanrdb.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaoverlap.o fastaoverlap.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastareformat.o fastareformat.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaremove.o fastaremove.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastarevcomp.o fastarevcomp.c fastadiff.c: In function 'fasta_diff': fastadiff.c:70:13: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 70 | comp = g_strcasecmp; @@ -2896,14 +2934,17 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastanrdb.o fastanrdb.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaoverlap.o fastaoverlap.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastareformat.o fastareformat.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastaremove.o fastaremove.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastarevcomp.o fastarevcomp.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasoftmask.o fastasoftmask.c +fastafetch.c: In function 'get_query_list': +fastafetch.c:121:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] + 121 | if(!g_strcasecmp(query, "stdin")){ + | ^~ +In file included from /usr/include/glib-2.0/glib.h:84, + from ../../src/general/argument.h:26, + from fastafetch.c:21: +/usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here + 203 | gint g_strcasecmp (const gchar *s1, + | ^~~~~~~~~~~~ fastaremove.c: In function 'Argument_main': -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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasort.o fastasort.c fastaremove.c:73:5: warning: 'g_strcasecmp' is deprecated [-Wdeprecated-declarations] 73 | if(!g_strcasecmp(remove_path, "stdin")){ | ^~ @@ -2913,11 +2954,18 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasoftmask.o fastasoftmask.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasort.o fastasort.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c -o fastasplit.o fastasplit.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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 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")) @@ -2940,8 +2988,12 @@ /usr/include/glib-2.0/glib/gstrfuncs.h:203:23: note: declared here 203 | 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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 +gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 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)); @@ -2952,30 +3004,21 @@ /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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -gcc -g -O2 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 -ffile-prefix-map=/build/exonerate-2.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/glib-2.0 -I/usr/lib/i386-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 make[3]: Leaving directory '/build/exonerate-2.4.0/src/util' make[3]: Entering directory '/build/exonerate-2.4.0/src' make[3]: Nothing to be done for 'all-am'. @@ -3120,7 +3163,7 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/exonerate/ - make -j8 install DESTDIR=/build/exonerate-2.4.0/debian/exonerate AM_UPDATE_INFO_DIR=no + make -j15 install DESTDIR=/build/exonerate-2.4.0/debian/exonerate AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/exonerate-2.4.0' Making install in doc make[2]: Entering directory '/build/exonerate-2.4.0/doc' @@ -3130,7 +3173,7 @@ make[4]: Entering directory '/build/exonerate-2.4.0/doc/man/man1' make[5]: Entering directory '/build/exonerate-2.4.0/doc/man/man1' make[5]: Nothing to be done for 'install-exec-am'. - /bin/mkdir -p '/build/exonerate-2.4.0/debian/exonerate/usr/share/man/man1' + /usr/bin/mkdir -p '/build/exonerate-2.4.0/debian/exonerate/usr/share/man/man1' /usr/bin/install -c -m 644 exonerate.1 ipcress.1 exonerate-server.1 fastautils.1 '/build/exonerate-2.4.0/debian/exonerate/usr/share/man/man1' make[5]: Leaving directory '/build/exonerate-2.4.0/doc/man/man1' make[4]: Leaving directory '/build/exonerate-2.4.0/doc/man/man1' @@ -3226,7 +3269,7 @@ make[4]: Entering directory '/build/exonerate-2.4.0/src/program' make[5]: Entering directory '/build/exonerate-2.4.0/src/program' make[5]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/exonerate-2.4.0/debian/exonerate/usr/bin' + /usr/bin/mkdir -p '/build/exonerate-2.4.0/debian/exonerate/usr/bin' /usr/bin/install -c exonerate ipcress exonerate-server '/build/exonerate-2.4.0/debian/exonerate/usr/bin' make[5]: Leaving directory '/build/exonerate-2.4.0/src/program' make[4]: Leaving directory '/build/exonerate-2.4.0/src/program' @@ -3234,8 +3277,8 @@ Making install in util make[3]: Entering directory '/build/exonerate-2.4.0/src/util' make[4]: Entering directory '/build/exonerate-2.4.0/src/util' - /bin/mkdir -p '/build/exonerate-2.4.0/debian/exonerate/usr/bin' make[4]: Nothing to be done for 'install-data-am'. + /usr/bin/mkdir -p '/build/exonerate-2.4.0/debian/exonerate/usr/bin' /usr/bin/install -c fastaclean fastaclip fastachecksum fastacomposition fastadiff fastaexplode fastafetch fastahardmask fastaindex fastalength fastanrdb fastaoverlap fastareformat fastaremove fastarevcomp fastasoftmask fastasort fastasplit fastasubseq fastatranslate fastavalidcds fasta2esd fastaannotatecdna esd2esi '/build/exonerate-2.4.0/debian/exonerate/usr/bin' make[4]: Leaving directory '/build/exonerate-2.4.0/src/util' make[3]: Leaving directory '/build/exonerate-2.4.0/src/util' @@ -3348,12 +3391,14 @@ 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/52864/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/52864/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/26390 and its subdirectories -I: Current time: Thu Jun 8 14:56:15 -12 2023 -I: pbuilder-time-stamp: 1686279375 +I: removing directory /srv/workspace/pbuilder/52864 and its subdirectories +I: Current time: Thu Jul 11 23:33:30 +14 2024 +I: pbuilder-time-stamp: 1720690410